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Leaf is an important organ of photosynthesis in plants, and leaf color has an important influence on photosynthesis. However, the molecular mechanisms of leaf color regulation are still unclear. In this study, we identified a rice (Oryza sativa) temperature sensitive albino trans-green (tag) mutant, which showed albino leaves at the seedling stage, and gradually turned green. Map-based cloning showed that TAG is a Novel allele gene of OsBT3, encoding an adenine nucleotide transport protein. Compared with the allele mutants of sla and wsl2, tag displayed some new phenotypes, such as it was a low-temperature-sensitive albino trans-green mutant with serious DNA damage in the albino leaves, and the PSI photosynthetic efficiency and photosynthesis of it were enhanced significantly in mature stage. Besides, we also found TAG was also localized in chloroplasts and played an important role on chloroplast development. Moreover, we newly discovered that TAG is highly expressed in L3U, which is induced by low temperature, and in situ hybridization results showed TAG expressed in the shoot apical meristem, leaf primordium and vascular bundle. Taken together, the above new results provide deeper clues to explain the molecular mechanisms by which TAG regulates chloroplast development. [ABSTRACT FROM AUTHOR]

In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield. [ABSTRACT FROM AUTHOR]

Zinc (Zn) deficiency, caused by inadequate Zn intake in the human diet, has serious health implications. Rice (Oryza sativa) is the staple food in regions with a high incidence of Zn deficiency, so raising Zn levels in rice grain could help alleviate Zn deficiency. The wild relatives of cultivated rice vary widely in grain Zn content and thus are suitable resources for improving this trait. However, few loci underlying grain Zn content have been identified in wild rice relatives. Here, we identified a major quantitative trait locus for grain Zn content, Grain Zn Content 1 (qGZnC1), from Yuanjiang common wild rice (Oryza rufipogon Griff.) using map-based cloning. Down-regulating GZnC1 expression reduced the grain Zn content, whereas the presence of GZnC1 had the opposite effect, indicating that GZnC1 is involved in grain Zn content in rice. Notably, GZnC1 is identical to a previously reported gene, EMBRYO SAC ABORTION 1 (ESA1), involved in seed setting rate. The mutation in GZnC1/ESA1 at position 1819 (T1819C) causes delayed termination of protein translation. In addition, GZnC1 is specifically expressed in developing panicles. Several genes related to Zn-transporter genes were up-regulated in the presence of GZnC1. Our results suggest that GZnC1 activates Zn transporters to promote Zn distribution in panicles. Our work thus sheds light on the genetic mechanism of Zn accumulation in rice grain and provides a new genetic resource for improving Zn content in rice. Key message: We identified an allele from the rice progenitor Oryza rufipogon, GZnC1, that influences grain zinc content. This allele is pleiotropic and is identical to EMBRYO SAC ABORTION 1, which is implicated in decreased seed setting rate. [ABSTRACT FROM AUTHOR]

To further understand the molecular mechanism for rice male reproduction, a rice male sterile mutant paa1 was screened from the rice mutant library generated by treatment with 60Coγ-rays. Genetic analysis revealed that paa1 is controlled by a single- recessive nuclear gene, and the anthers of the paa1 mutant were smaller than those of WT plants with a white color. Histological analysis demonstrated that the anthers of the paa1 mutant began to turn abnormal at the microspore stage after meiosis, with abnormal degradation of tapetum, deformed Ubisch bodies, and defective pollen exine. TUNEL assay results also confirmed the delay of tapetum PCD in paa1. Map-based cloning was performed for the PAA1 location. As a result, PAA1 was located in a 88-kb region at the end of chromosome 10, which comprises a total of seven candidate genes, and no genes related to anther development have been reported in this region. The results indicate that PAA1 is an essential gene in regulating tapetum development and pollen/microspore formation after rice meiosis. [ABSTRACT FROM AUTHOR]

Rice false smut (RFS), an emerging major fungal disease worldwide caused by Ustilaginoidea virens, affects rice grain quality and yield. RFS cause 2.8–49% global yield loss depending upon disease severity and cultivars. In India, the yield loss due to RFS ranged from 2 to 75%. Identification of the genes or quantitative trait loci (QTLs) governing disease resistance would be of utmost importance towards mitigating the economic losses incurred due to RFS. Here, we report mapping of RFS resistance QTLs from a resistant breeding line RYT2668. The mapping population was evaluated for RFS resistance under the field condition in three cropping seasons 2013, 2015, and 2016. A positive correlation among infected panicle/plant, total smut ball/panicle, and disease score was observed in the years 2013, 2015, and the mean data. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 using 2326 single nucleotide polymorphism markers. Of these, two QTLs, qRFSr5.3 and qRFSr7.1a, were associated with the infected panicle per plant, one QTL qRFsr9.1 with total smut ball per panicle, and four QTLs qRFSr2.2, qRFSr4.3, qRFSr5.4, and qRFSr7.1b with disease score. Among them, a novel QTL qRFSr9.1 on chromosome 9 exhibits the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 revealed four nucleotide-binding sites–leucine-rich repeat (NBS-LRR) domain-containing disease resistance proteins. In summary, our findings mark the hotspot region of rice chromosomes carrying genes/QTLs for resistance to the RFS disease. [ABSTRACT FROM AUTHOR]

Key message: A novel genic male-sterile mutant ms40 was obtained from EMS treated RP125. The key candidate gene ZmbHLH51 located on chromosome 4 was identified by map-based cloning. This study further enriched the male sterile gene resources for both production applications and theoretical studies of abortion mechanisms. Maize male-sterile mutant 40 (ms40) was obtained from the progeny of the ethyl methanesulfonate (EMS) treated inbred line RP125. Genetic analysis indicated that the sterility was controlled by a single recessive nuclear gene. Cytological observation of anthers revealed that the cuticles of ms40 anthers were abnormal, and no Ubisch bodies were observed on the inner surface of ms40 anthers through scanning electron microscopy(SEM). Moreover, its tapetum exhibited delayed degradation and then blocked the formation of normal microspores. Using map-based cloning strategy, the ms40 locus was found to locate in a 282-kb interval on chromosome 4, and five annotated genes were predicted within this region. PCR-based sequencing detected a single non-synonymous SNP (G > A) that changed glycine (G) to arginine (A) in the seventh exon of Zm00001d053895, while no sequence difference between ms40 and RP125 was found for the other four genes. Zm00001d053895 encodes the bHLH transcription factor ZmbHLH51 which is localized in the nucleus. Phylogenetic analysis showed that ZmbHLH51 had the highest homology with Sb04g001650, a tapetum degeneration retardation (TDR) bHLH transcription factor in Sorghum bicolor. Co-expression analysis revealed a total of 1192 genes co-expressed with ZmbHLH51 in maize, 647 of which were anther-specific genes. qRT-PCR results suggested the expression levels of some known genes related to anther development were affected in ms40. In summary, these findings revealed the abortion characteristics of ms40 anthers and lay a foundation for further studies on the mechanisms of male fertility. [ABSTRACT FROM AUTHOR]

Background: The rice (Oryza sativa) gene Xa7 has been hypothesized to be a typical executor resistance gene against Xanthomonas oryzae pv. oryzae (Xoo), and has conferred durable resistance in the field for decades. Its identity and the molecular mechanisms underlying this resistance remain elusive. Results: Here, we filled in gaps of genome in Xa7 mapping locus via BAC library construction, revealing the presence of a 100-kb non-collinear sequence in the line IRBB7 compared with Nipponbare reference genomes. Complementary transformation with sequentially overlapping subclones of the BACs demonstrated that Xa7 is an orphan gene, encoding a small novel protein distinct from any other resistance proteins reported. A 27-bp effector binding element (EBE) in the Xa7 promoter is essential for AvrXa7-inducing expression model. XA7 is anchored in the endoplasmic reticulum membrane and triggers programmed cell death in rice and tobacco (Nicotiana benthamiana). The Xa7 gene is absent in most cultivars, landraces, and wild rice accessions, but highly homologs of XA7 were identified in Leersia perrieri, the nearest outgroup of the genus Oryza. Conclusions: Xa7 acts as a trap to perceive AvrXa7 via EBEAvrXa7 in its promoter, leading to the initiation of resistant reaction. Since EBEAvrXa7 is ubiquitous in promoter of rice susceptible gene SWEET14, the elevated expression of which is conducive to the proliferation of Xoo, that lends a great benefit for the Xoo strains retaining AvrXa7. As a result, varieties harboring Xa7 would show more durable resistance in the field. Xa7 alleles analysis suggests that the discovery of new resistance genes could be extended beyond wild rice, to include wild grasses such as Leersia species. [ABSTRACT FROM AUTHOR]

Key message: A novel MADS-box member SiMADS34 is essential for regulating inflorescence architecture and grain yield in Setaria italica. MADS-box transcription factors participate in regulating various developmental processes in plants. Inflorescence architecture is one of the most important agronomic traits and is closely associated with grain yield in most staple crops. Here, we isolated a panicle development mutant simads34 from a foxtail millet (Setaria italica (L.) P. Beauv.) EMS mutant library. The mutant showed significantly altered inflorescence architecture and decreased grain yield. Investigation of agronomic traits revealed increased panicle width by 16.8%, primary branch length by 10%, and number of primary branches by 30.9%, but reduced panicle length by 25.2%, and grain weight by 25.5% in simads34 compared with wild-type plants. Genetic analysis of a simads34 × SSR41 F2 population indicated that the simads34 phenotype was controlled by a recessive gene. Map-based cloning and bulked-segregant analysis sequencing demonstrated that a single G-to-A transition in the fifth intron of SiMADS34 in the mutant led to an alternative splicing event and caused an early termination codon in this causal gene. SiMADS34 mRNA was expressed in all of the tissues tested, with high expression levels at the heading and panicle development stages. Subcellular localization analysis showed that simads34 predominantly accumulated in the nucleus. Transcriptome sequencing identified 241 differentially expressed genes related to inflorescence development, cell expansion, cell division, meristem growth and peroxide stress in simads34. Notably, an SPL14–MADS34–RCN pathway was validated through both RNA-seq and qPCR tests, indicating the putative molecular mechanisms regulating inflorescence development by SiMADS34. Our study identified a novel MADS-box member in foxtail millet and provided a useful genetic resource for inflorescence architecture and grain yield research. [ABSTRACT FROM AUTHOR]

Trichomes are hair-like structures derived from plant epidermal cells. Trichomes exist in most plant species and are categorized as either glandular or non-glandular. Glandular trichomes function as chemical protection against herbivores, while non-glandular trichomes serve as physical barriers to various biotic and environmental stresses. Here, we describe a novel recessive mutation named hairless on stems (host) which was identified based on the absence of trichomes on stems. host plants exhibited lower density of trichomes on leaves, stems, and hypocotyls, compared with the wild-type (WT) plants. Types I, III, and V trichomes, especially, were not developed at all on the stems of the host plants. In addition to trichome initiation, the length of Type I trichomes was shorter in the host plants than in the WT plants. The growth of host plants under greenhouse conditions showed that the mutant has shorter stems and fewer leaves than the WT plants. Genetic mapping of the host locus using the map-based cloning approach positioned the locus within 4.4 cM interval flanked by markers, Solyc09g074280 and Solyc09g075360, on chromosome 9. The identification of the Host gene will provide a clue for understanding multicellular trichome development in tomato and the Host gene can be used as a useful genetic resource to develop insect-resistant tomato. [ABSTRACT FROM AUTHOR]

Background: The chloroplast signal recognition particle 54 (cpSRP54) is known for targeting the light-harvesting complex proteins to thylakoids and plays a critical role for chloroplast development in Arabidopsis, but little is known in rice. Here, we reported two homologous cpSRP54s that affect chloroplast development and plant survival in rice. Results: Two rice cpSRP54 homologues, OscpSRP54a and OscpSRP54b, were identified in present study. The defective OscpSRP54a (LOC_Os11g05552) was responsible for the pale green leaf phenotype of the viable pale green leaf 14 (pgl14) mutant. A single nucleotide substitution from G to A at the position 278, the first intron splicing site, was detected in LOC_Os11g05552 in pgl14. The wild type allele could rescue the mutant phenotype. Knockout lines of OscpSRP54b (LOC_Os11g05556) exhibited similar pale green phenotype to pgl14 with reduced chlorophyll contents and impaired chloroplast development, but showed apparently arrested-growth and died within 3 weeks. Both OscpSRP54a and OscpSRP54b were constitutively expressed mainly in shoots and leaves at the vegetative growth stage. Subcellular location indicated that both OscpSRP54a and OscpSRP54b were chloroplast-localized. Both OscpSRP54a and OscpSRP54b were able to interact with OscpSRP43, respectively. The transcript level of OscpSRP43 was significantly reduced while the transcript level of OscpSRP54b was apparently increased in pgl14. In contrast, the transcript levels of OscpSRP54a, OscpSRP43 and OscpSRP54b were all significantly decreased in OscpSRP54b knockout lines. Conclusion: Our study demonstrated that both OscpSRP54a and OscpSRP54b were essential for normal chloroplast development by interacting with OscpSRP43 in rice. OscpSRP54a and OscpSRP54b might play distinct roles in transporting different chloroplast proteins into thylakoids through cpSRP-mediated pathway. [ABSTRACT FROM AUTHOR]

The accumulation of carotenoids is related to pigment formation in flowers and other organs. In order to elucidate the genetic variation of flower color in cauliflower, a F2 segregating population was obtained from yellow-flowered cauliflower 'QGS' and white-flowered Chinese kale 'JYJ'. Bulked segregant analysis combined with the whole-genome resequencing was employed to locate the target region for Flower Color. In this study, Bofc was anchored on chromosome C03 with a single peak, and further mapped to 164 kb interval with 0.28 cM genetic distance. BoCCD4, encoding carotenoid cleavage dioxygenase 4 in the carotenoid metabolic pathway, was selected as the most likely candidate gene. Sequence analysis revealed that an insertion of a 10,608 bp CACTA-like transposon in the coding region led to the loss-of-function of the BoCCD4 gene in cauliflower. These results will provide further understanding of the genetic mechanism controlling flower color in Brassica oleracea species. [ABSTRACT FROM AUTHOR]

DNA methylation pattern is found to be established by the combined actions of DNA methylation and demethylation. Compared to the DNA methylation pathway, DNA demethylation pathway, however, remains largely unknown. To better understand the DNA demethylation pathway, we performed genetic screening for Arabidopsis mutants with increased genomic DNA methylation levels through a 2 × 35S:LUC (LUC, luciferase) reporter system. A mutant with reduced LUC luminescence was identified by such a system, therefore named rll3-1 (for reduced LUC luminescence 3-1). The rll3-1 mutant exhibited pleiotropic developmental defects, such as delayed bolting as well as flowering, more branches, etc. By map-based cloning approach, rll3 locus that contains a single nuclear recessive mutation as revealed by the genetic analysis was mapped to a region between molecular markers CL102_B1 M1 and CL102_B3M1, which are located in bacterial artificial chromosome (BAC) clones F9P14 and F12K11, respectively, on chromosome 1. Chop-PCR analysis indicated that a total of seven tested loci displayed elevated DNA methylation levels. Whole-genome bisulfite sequencing further revealed 1536 loci exhibiting increased DNA methylation levels relative to Col-LUC control, among which there are 507 such loci overlapping between the rll3-1 and ros1-7 mutants, suggestive of a functional association between RLL3 and REPRESSOR OF SILENCING 1 (ROS1). Further investigations demonstrated that the expression levels of a few genes (like ROS1, IDM1, etc.), which are involved in DNA demethylation pathway, remained unchanged in the rll3-1 mutant, indicating that the increased DNA methylation levels in rll3-1 mutant are not attributable to downregulation of such genes. Taken together, our studies provide a demonstration of the involvement of RLL3 in the DNA demethylation pathway. [ABSTRACT FROM AUTHOR]

Key message: PE1 is a valuable locus synergistically regulating both P acquisition and utilization efficiency. Phosphorus (P) is required for crop production, particularly for soybean, due to its high protein and oil contents, and large demands for P in biological nitrogen fixation. Therefore, enhancing P efficiency is a practical and important target for soybean-breeding programs; however, the genetic mechanisms are still unclear. Previously, we identified a phosphorus efficiency locus 1 (PE1) in soybean through field evaluation. Here, fine mapping of PE1 was conducted in field using an expanded RIL population containing 168 F9:11 families derived from the same parents, BX10 and BD2. A high-resolution genetic map covering a 67.39 cM genetic region in a ~ 20.1 M physical region was constructed using 117 bin markers from chromosome 11, and scaffolds-21 and -32. The results revealed that PE1 was comprised of 15 QTLs for 11 of 18 tested traits, all of which could be detected under both P-deficient and P-sufficient conditions. Through map-based cloning, PE1 was further delimited to a 200-kb region located on scaffold-32, where 16 candidate genes were predicted for the PE1 locus. A set of NILs were also evaluated in P-deficient field conditions, with the results that P content and grain yield were 27.9% and 74.8% higher, respectively, and 25.4% more P was allocated to reproductive tissues in #pe1 than in #PE1 plants. The results herein suggest that PE1 is a valuable locus underlying both P absorption and utilization efficiency, which may be directly applicable in breeding programs seeking to develop elite P-efficient soybean varieties. [ABSTRACT FROM AUTHOR]

Key message: Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development. Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3′ region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development. [ABSTRACT FROM AUTHOR]

Verticillium wilt is a devastating disease caused by the soil-borne fungus Verticillium dahliae that causes severe wilt symptoms in more than 400 plant species, including economically important cotton. However, the molecular mechanism of plant resistance to Verticillium remains unclear. In this study, we identified an Arabidopsis mutant, vsad1 (verticillium sensitive and anthocyanin deficient 1), which showed more serious disease symptoms such as discoloration and chlorosis than wild-type Arabidopsis. vsad1 is a previously identified allele of the transparent testa 4 gene (tt4), which encodes chalcone synthase (CHS), a key enzyme involved in the biosynthesis of flavonoids. Our results showed that VSAD1 expression was induced in response to Verticillium dahliae infection. Overexpression of VSAD1 partially recovered the anthocyanin accumulation phenotype of the vsad1-1 mutant. The concentration of V. dahliae increased and ROS accumulation decreased in the vsad1 mutant after infection with V. dahliae. Knockdown of the homologous gene GhCHS in cotton plants increased their susceptibility to V. dahliae infection. Thus, we conclude that VSAD1 is involved in the regulation of plant resistance to Verticillium wilt. [ABSTRACT FROM AUTHOR]

Key message: 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. Abstract: 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. [ABSTRACT FROM AUTHOR]

Hybridization technology has proven valuable in enhancing yields in many crops, but was only recently adopted in the small grain cereals. Hybrid varieties in barley (Hordeum vulgare) rely on the cytoplasmic male sterility (CMS) system msm1 derived from Hordeum vulgare ssp. spontaneum. The major restorer gene described for the msm1 system is known as Rfm1 and maps to the top of chromosome 6H. To gain further insight into mechanisms underlying male fertility restoration in barley, we used a mapbased cloning approach to identify the nuclear gene involved in the restoration mechanism of this hybridization system. Taking advantage of the available genomic resources in barley in combination with a custom-made non-gridded BAC library developed from a restorer line, we cloned and sequenced the Rfm1 restorer locus. The characterization and annotation of the nucleotide sequence for the Rfm1 restorer allele allowed for the identification of the candidate gene for Rfm1. The Rfm1 locus carries a tandem repeat of a gene encoding a pentatricopeptide repeat (PPR) protein. Surprisingly, Rfm1 belongs to the PLS-DYW subfamily of PPR genes known for their involvement in RNA editing in plants organelles, but that to date have not been identified as restorer genes. [ABSTRACT FROM AUTHOR]

Trichomes are hair-like structures on the aerial surface of many plant species. Trichomes are well characterized for their role as physical barriers and chemical defense against herbivore attack. Here, we describe the characterization of a monogenic recessive mutant of tomato ( Solanum lycopersicum) called inquieta ( ini). All trichome types on ini plants showed distinct morphological defects (e.g., swelling) that are known to be associated with defects in the actin cytoskeleton. Genetic mapping experiments positioned the Ini locus within a 1.5 cM interval on chromosome 11 that contains the tomato homolog of the Arabidopsis ARPC2A gene, which encodes a protein involved in nucleating the polymerization of actin filaments. Use of ARPC2A as a molecular marker showed that this gene strictly co-segregates with the target locus in a mapping population of 135 F plants. Reverse transcriptase (RT)-PCR and genomic PCR experiments showed that full-length ARPC2A is amplified in wild-type but not in the ini mutant. Flanking PCR and Southern blot analysis showed that the ini mutation corresponds to a complex ∼6-kb insertion in the 5 intron of ARPC2A. These results provide molecular evidence that altered trichome development in the ini mutant is caused by a defect in actin cytoskeleton formation. [ABSTRACT FROM AUTHOR]

Leaf morphology of rice ( Oryza sativa L.) is an important agronomic trait that greatly affects the total grain yield. In the present study, a mutant with screw flag leaf 1 ( sfl1) was identified and characterized. The sfl1 mutants showed the screw flag leaf and panicle-at-bottom phenotype at reproductive stage, accompanied by a dramatic reduced plant height, flag leaf length and width, panicle length, and grain width. Histological analysis showed that the sfl1 mutant had increased small veins and number and size of bulliform cells compared with wild-type. Genetic analysis suggested that the mutant traits were completely controlled by a single recessive gene. The SFL1 gene was mapped to the long arm of chromosome 10 within a region of 49.7 kb between InDel markers B7P26 and B7P31. Cloning and sequencing results revealed that there was only one base substitution in the second exon of candidate gene Os10g0416200. The SFL1 locus encodes the 3-ketoacyl-CoA synthase 20 protein (KCS20). Furthermore, 288 KCS genes from 11 flowering plant species were identified using bioinformatics approaches. The qRT-PCR analysis showed that SFL1 was highly expressed in sheath, flag leaf and panicles. Furthermore, ROLLED and ERECT LEAF 2 ( REL2), NARROW AND ROLLED LEAF 1 ( NRL1), LEAF INCLINATION 2 ( LC2), a zinc finger homeodomain class homeobox transcription factors gene ( OsZHD1), ADAXIALIZED LEAF 1 ( ADL1), ABAXIALLY CURLING LEAF 1 ( ACL1), Rice outermost cell-specific gene 5 ( Roc5), and ROLLED and ERECT LEAF 1 ( REL1) were significantly upregulated while ROLLED LEAF 14 ( RL14) was significantly downregulated in sfl1 mutant. These results provide an important basis for the functional analysis of SFL1 gene in rice leaf and panicle development, as well as exploration of further mechanisms controlling screw flag leaf trait for application in rice breeding. [ABSTRACT FROM AUTHOR]

Background: Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice ( Oryza sativa L.). Sugary endosperm, sugary-1 ( sug-1), is a mutant trait for starch biosynthesis. Rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. Although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent problems in milling. This study was conducted to identify the genes responsible for the sug-h phenotype through a map-based cloning technology. Results: We induced a mild sugary mutant, sugary-h ( sug-h) through the chemical mutagenesis on the Korean japonica cultivar Hwacheong. Grains of the sug-h mutant were translucent and amber-colored, and the endosperm appeared less wrinkled than sug-1, whereas the soluble sugar content was fairly high. These characteristics confer greater marketability to the sug-h mutant. Genetic analyses indicated that the sug-h mutant phenotype was controlled by a complementary interaction of two recessive genes, Isoamylase1 ( OsISA1), which was reported previously, and Starch branching enzyme IIa ( OsBEIIa), which was newly identified in this study. Complementation tests indicated that OsBEIIa regulated the properties of sugary endosperm . Conclusions: Complementary interactions between the starch biosynthesis genes OsISA1 and OsBEIIa determine the mild sugary endosperm mutant, sugary-h, in rice. Our finding may facilitate the breeding of sugaryendosperm rice for commercial benefit. [ABSTRACT FROM AUTHOR]

Blue light receptor phot1 and phot2 regulate hypocotyl phototropism induced by high intensity blue light (HBL) in functional redundancy. The phenotype of rpt2 single mutant is similar with double mutant phot1phot2 that lost phototropism, but rpt2phot1 double mutant shows normal phototropic response, which indicating that phot1 has dual opposite function with inducing and inhibiting hypocotyls phototropism. However, the mechanism of phot1-mediated inhibition remains to be elucidated. Here, we screened mutants with phototropism from EMS mutagenesis of rpt2 and cloned the gene P1SA1 (Phototropin1 Signaling Associated 1), which maybe locate downstream of phot1 and function in regulating phot1-mediated inhibitory response. The rpt2 p1sa1 mutant shows normal phototropism to unilateral HBL and overexpression of PHOT1 in rpt2 p1sa1 lost hypocotyl phototropism again, which indicated that P1SA1 may be the allelic of PHOT1. These results will open new perspectives about the screening and identification of genes involved in phot1-mediated inhibitory response, and provide theoretical basis for the self-regulation mechanism of plant to reduce high light damage. [ABSTRACT FROM AUTHOR]

Main conclusion: The map-based cloning and application of a flower organ number gene twin - grain1 provide great potential for improving seed production in hybrid rice. Abstract: A new germplasm for high-yield rice breeding, the twin- grain1 ( tg1) mutant with more than one grain in a glume, was obtained from the Zhejing 22 rice variety via physical mutagenesis. The mapping results showed that TG1 is allelic to FLORAL ORGAN NUMBER2 (FON2)/FLORAL ORGAN NUMBER4 (FON4), a flower organ number gene located at 88.7 cM on chromosome 11. The novel tg1 gene allele was introgressed into the cytoplasmic male sterility (CMS) line Zhejing 22A, giving rise to a new CMS line Zhejing 22- tg1A. The Zhejing 22- tg1A line showed enhanced glume opening and stigma exsertion, which increased the outcrossing rate in hybrid rice. A small-scale hybrid rice seed production test demonstrated that the grain yield of the Zhejing 22- tg1A/Zhejinghui 5 line was significantly increased compared to that of the Zhejing 22A/Zhejinghui 5 line. The plot yield evaluation of the F hybrid lines showed a higher yield for the Zhejing 22- tg1A/Zhejinghui 5 line than that of the Zhejing 22A/Zhejinghui 5 line. The results implied great potentials for the tg1 gene in hybrid rice breeding. [ABSTRACT FROM AUTHOR]

Main conclusion : Young Seedling Stripe1 (YSS1) was characterized as an important regulator of plastid-encoded plastid RNA polymerase (PEP) activity essential for chloroplast development at rice seedling stage. Chloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although a few regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. Here, we report the characterization of a temperature-sensitive young seedling stripe1 ( yss1) rice mutant, which develops striated leaves at the seedling stage, particularly in leaf 3, but produces wild-type leaves in leaf 5 and onwards. The chlorotic leaves have decreased chlorophyll (Chls) accumulation and impaired chloroplast structure. Positional cloning combined with sequencing demonstrated that aberrant splicing of the 8th intron in YSS1 gene, due to a single nucleotide deletion around splicing donor site, leads to decreased expression of YSS1 and accumulation of an 8th intron-retained yss1 transcript. Furthermore, complementation test revealed that downregulation of YSS1 but not accumulation of yss1 transcript confers yss1 mutant phenotype. YSS1 encodes a chloroplast nucleoid-localized protein belonging to the DUF3727 superfamily. Expression analysis showed that YSS1 gene is more expressed in newly expanded leaves, and distinctly up-regulated as temperatures increase and by light stimulus. PEP- and nuclear-encoded phage-type RNA polymerase (NEP)-dependent genes are separately down-regulated and up-regulated in yss1 mutant, indicating that PEP activity may be impaired. Furthermore, levels of chloroplast proteins are mostly reduced in yss1 seedlings. Together, our findings identify YSS1 as a novel regulator of PEP activity essential for chloroplast development at rice seedling stage. [ABSTRACT FROM AUTHOR]

The chromogen gene C is critical for anthocyanin regulation in rice, and apiculus color is an important agronomic trait in selective breeding and variety purification. Mapbased cloning and in-depth functional analysis of the C gene will be useful for understanding the molecular mechanism of anthocyanin biosynthesis and for rice breeding. Japonica landrace Lijiangxintuanheigu (LTH) has red apiculi and purple stigmas. Genetic analysis showed that red apiculus and purple stigma in LTH co-segregated indicating control by a single dominant gene, or by two completely linked genes. Using 1,851 recessive individuals from two F populations, the target gene OsC was delimited to a 70.8 kb interval on chromosome 6 that contains the rice homologue of the maize anthocyanin regulatory gene C1. When the entire OsC gene and its full-length cDNA cloned from LTH were transformed into japonica cultivar Kitaake with colorless apiculi and stigmas all positive transformants had red apiculi but non-colored stigmas, validating that OsC alone was responsible for the apiculus color and represented the functional C gene. OsC was constitutively expressed in all tissues examined, with strongest expression in leaf blades. These results set a foundation to clarify the regulatory mechanisms of OsC in the anthocyanin biosynthetic pathway. [ABSTRACT FROM AUTHOR]

Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change. Genetic analysis of reciprocal crosses between wsl12 and wild-type plants showed that wsl12 was a recessive mutant in a single nuclear locus. Map-based cloning revealed that the WSL12 locus encoded OsNDPK2, one of the three nucleoside diphosphate kinases (OsNDPKs). WSL12 expressed in all tested tissues, while it highly expressed in leaves and young tissues. The WSL12 protein localized to the chloroplast. Thewsl12mutant showed higher superoxide anion level and enhanced sensitivity to abscisic acid (ABA) and salinity. The transcription pattern of many genes involved in chlorophyll biosynthesis, ABA synthesis, light signaling pathway, reactive oxygen species-scavenging pathway and the other two OsNDPKs was altered in the wsl12 mutant. These results indicate that the OsNDPK2 encoded by WSL12 plays an important role in chloroplast development and chlorophyll biosynthesis by regulating the expression levels of related genes. In addition, WSL12 also affects the response to abiotic stress, such as ABA and salinity in rice, and is beneficial to molecular breeding of stress tolerance. [ABSTRACT FROM AUTHOR]

Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change. Genetic analysis of reciprocal crosses between wsl12 and wild-type plants showed that wsl12 was a recessive mutant in a single nuclear locus. Map-based cloning revealed that the WSL12 locus encoded OsNDPK2, one of the three nucleoside diphosphate kinases (OsNDPKs). WSL12 expressed in all tested tissues, while it highly expressed in leaves and young tissues. The WSL12 protein localized to the chloroplast. The wsl12 mutant showed higher superoxide anion level and enhanced sensitivity to abscisic acid (ABA) and salinity. The transcription pattern of many genes involved in chlorophyll biosynthesis, ABA synthesis, light signaling pathway, reactive oxygen species-scavenging pathway and the other two OsNDPKs was altered in the wsl12 mutant. These results indicate that the OsNDPK2 encoded by WSL12 plays an important role in chloroplast development and chlorophyll biosynthesis by regulating the expression levels of related genes. In addition, WSL12 also affects the response to abiotic stress, such as ABA and salinity in rice, and is beneficial to molecular breeding of stress tolerance. [ABSTRACT FROM AUTHOR]

Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is SnTox3, which evokes programmed cell death and leads to disease when recognized by the wheat Snn3- B1 gene. Here, we developed saturated genetic linkage maps of the Snn3- B1 region using two F populations derived from the SnTox3-sensitive line Sumai 3 crossed with different SnTox3-insensitive lines. Markers were identified and/or developed from various resources including previously mapped simple sequence repeats, bin-mapped expressed sequence tags, single nucleotide polymorphisms, and whole genome survey sequences. Subsequent high-resolution mapping of the Snn3- B1 locus in 5600 gametes delineated the gene to a 1.5 cM interval. Analysis of micro-colinearity of the Snn3- B1 region indicated that it was highly disrupted compared to rice and Brachypodium distachyon. The screening of a collection of durum and common wheat cultivars with tightly linked markers indicated they are not diagnostic for the presence of Snn3- B1, but can be useful for marker-assisted selection if the SnTox3 reactions of lines are first determined. Finally, we developed an ethyl methanesulfonate-induced mutant population of Sumai 3 where the screening of 408 M families led to the identification of 17 SnTox3-insensitive mutants. These mutants along with the markers and high-resolution map developed in this research provide a strong foundation for the map-based cloning of Snn3- B1, which will broaden our understanding of the wheat- P. nodorum system and plant-necrotrophic pathogen interactions in general. [ABSTRACT FROM AUTHOR]

Proper chloroplast development and chlorophyll biosynthesis are essential for the photoautotrophic plants. The insertion of magnesium (Mg) into protoporphyrin IX (Proto), catalyzed by magnesium chelatase (Mg-chelatase), is the first committed step of chlorophyll biosynthesis. In dicot plants, a proposed model revealed that Mg-chelatase I subunit (CHLI) and Mg-chelatase D subunit (CHLD) can interact directly; however, their relation remains elusive in rice, a monocot model plant. In this study, we characterized a chlorophyll-deficiency mutant, etiolated leaf and lethal ( ell), which displayed a yellow leaf in young seedlings and became lethal after three-leaf stage. Chlorophyll content in homozygous ell mutant was approximately 1 % of that in the wild type. Besides, chloroplast development in the mutant was entirely arrested and no thylakoid structure was observed. By map-based cloning, the ell locus was delimited to a 3.9-Mb interval in chromosome 3. A single-base mutation (G529C) in OsCHLI was identified, leading to an amino acid substitution (G177R) in a highly conserved region. Compared with the wild type, more Proto but less magnesium protoporphyrin IX (Mg-Proto) was measured in the ell mutant. Using protoplast transfection and callus transformation, we found that exogenous OsCHLI could consistently recover the lesion of chloroplast in the ell mutant. By subcellar localization analysis, OsCHLI was detected in the chloroplast. Despite the secondary structure of OsCHLI that was predicted to be altered in the mutant, the point mutation did not affect subcellular localization. Real-time PCR demonstrated that the ell mutation induced significantly transcriptional downregulation of the photosynthesis-associated nuclear and plastid genes. Additionally, yeast-two-hybrid experiments indicated that the single amino acid substitution blocked the intrinsic interaction between OsCHLI and OsCHLD. Moreover, OsCHLI showed physical interactions with some thioredoxins (TRXs), suggesting a similar regulatory mechanism of Mg-chelatase activity in both monocot and dicot plants. [ABSTRACT FROM AUTHOR]

Main conclusion: The involvement of OsKASI in FA synthesis is found to play a critical role in root development of rice. The root system plays important roles in plant nutrient and water acquisition. However, mechanisms of root development and molecular regulation in rice are still poorly understood. Here, we characterized a rice ( Oryza sativa L.) mutant with shortened roots due to a defect in cell elongation. Map-based cloning revealed that the mutation occurred in a putative 3-oxoacyl-synthase, an ortholog of β-ketoacyl-[acyl carrier protein] synthase I (KASI) in Arabidopsis, thus designated as OsKASI. OsKASI was found to be ubiquitously expressed in various tissues throughout the plant and OsKASI protein was localized in the plastid. In addition, OsKASI deficiency resulted in reduced fertility and a remarkable change in fatty acid (FA) composition and contents in roots and seeds. Our results demonstrate that involvement of OsKASI in FA synthesis is required for root development in rice. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) blast caused by fungus Magnaporthe oryzae is one of the most devastating diseases throughout the world. In the current study, a rice blast resistance gene, designated as Pike, was identified from an indica breeding line Xiangzao143 conferring a durable resistance to rice blast. A map-based cloning strategy was then employed to locate Pike to a 306-kb genomic interval in proximity of the telomeric region of the long arm of chromosome 11. Candidate gene analysis and transgenic complementation test demonstrated that two Xiangzao143-derived adjacent CC–NBS–LRR genes (Pike-1 and Pike-2) at the previously identified Pik locus were required for the Pike-mediated resistance. As compared to the previously identified Pik alleles, the putative Pike-1 peptide was found to be unique in three highly polymorphic sites, two amino acid residue sites (D153 and D229) in the CC domain and one site (L442-W443-P465) in the NBS domain. In addition, against a set of 215 M. oryzae isolates collected from diverse rice cropping areas of China, the Pike carrier Xiangzao143 showed a unique resistance spectrum and a high resistance frequency of 86.1 %. These results thus declared Pike as a novel allele of the Pik locus. Two SNPs G1328C and A3017T in Pike DNA sequence were identified and based on the SNPs, two Pike-specific dCAPS markers d-G1328C and d-A3017T were developed and have been used to effectively distinguish Pike from all of the previously identified Pik alleles. [ABSTRACT FROM AUTHOR]

Plant architecture directly affects biomass in higher plants, especially grain yields in agricultural crops. In this study, we characterized a recessive mutant, plant architecture determinant ( pad), derived from the Oryza sativa ssp. indica cultivar MH86. The mutant exhibited severe dwarf phenotypes, including shorter and stunted leaves, fewer secondary branches during both the vegetative and reproductive growth stages. Cytological studies revealed that pad mutant growth defects are primarily due to the inhibition of cell expansion. The PAD gene was isolated using a map-based cloning strategy. It encodes a plasma membrane protein OsMCA1 and a SNP responsible for a single amino acid change was found in the mutant. PAD was universally expressed in rice tissues from the vegetative to reproductive growth stages, especially in seedlings, nodes and rachillae. Quantitative real-time PCR analysis revealed that the most of the genes responding to gibberellin (GA) metabolism were up-regulated in pad mutant internodes. The endogenous GA content measurement revealed that the levels of GA were significantly decreased in the third internode of pad mutants. Moreover, a GA response assay suggested that OsMCA1/PAD might be involved in the regulation of GA metabolism and signal transduction. Our results revealed the pad is a loss-of-function mutant of the OsMCA1/PAD, leading to upregulation of genes related to GA deactivation, which decreased bioactive GA levels. [ABSTRACT FROM AUTHOR]

A dense panicle mutant ( dp2) derived from the Oryza sativa ssp. japonica cultivar Nipponbare through ethyl methane sulfonate mutagenesis was used in present study. Compared to the wild type, the panicle of dp2 mutant exhibited more branches and denser grains. Further more, the number of spikelets per panicle, number of primary branches and secondary branches of dp2 mutant were significantly increased while the panicle length, and 1,000-grain weight were significantly decreased. The results from the genetic analysis indicated that the dense panicle phenotype was controlled by a single dominance nuclear gene. Polymorphic analysis of SSR and InDel markers demonstrated that the DP2 gene was located at the long arm of chromosome 2, which was further mapped between SSR markers RM341 and RM13356 in a physical region of 398 kb. Within this region, the RCN2 (LOC_Os02g32950) gene which was annotated relating to the development of rice panicle was found. Compared to the wild type, the sequence of RCN2 gene in the dp2 mutant showed that two SNPs replacement had taken place in the promoter region (G-A) and the intron region (A-T), respectively. The dp2 mutant could be a novel mutant of RCN2 gene and this novel mutant might be useful for further studies on this gene. [ABSTRACT FROM AUTHOR]

The columnar growth habit of apple trees ( Malus × domestica Borkh.) is a unique plant architecture phenotype that arose as a bud sport mutation of a McIntosh tree in the 1960s. The mutation (' Co gene') led to trees (McIntosh Wijcik) with thick, upright main stems and short internodes that generate short fruit spurs instead of long lateral branches. Although Co has been localized to chromosome 10, in a region approximately between 18.5 and 19 Mb, its molecular nature is unknown. In a classical positional cloning approach in combination with the analysis of NGS data, we cloned and analyzed the Co region. Our results show that the insertion of a Ty3/Gypsy retrotransposon into a non-coding region at position 18.8 Mb is the only detectable genomic difference between McIntosh and McIntosh Wijcik and is found in all columnar cultivars. The genetic effect of the insertion is unclear; however, Illumina RNA-seq data of McIntosh and McIntosh Wijcik suggest that the columnar growth habit is associated with differential expression of the retrotransposon transcript, causing changes in the expression levels of many protein coding genes. The mechanism by which the Gypsy retrotransposon is involved in generating the columnar habit is not yet clear; our findings form the basis for tackling this question. [ABSTRACT FROM AUTHOR]

Barley yellow dwarf disease (BYD) is transmitted by aphids and is caused by different strains of Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV). Economically it is one of the most important diseases of cereals worldwide. Besides chemical control of the vector, growing of tolerant/resistant cultivars is an effective way of protecting crops against BYD. The Ryd3 gene in barley ( Hordeum vulgare L.) confers tolerance to BYDV-PAV and BYDV-MAV and the locus was previously mapped on the short arm of barley chromosome 6H near the centromere. We applied a strategy for high-resolution mapping and marker saturation at the Ryd3 locus by exploiting recent genomic tools available in barley. In a population of 3,210 F2 plants, 14 tightly linked markers were identified, including 10 that co-segregated with Ryd3. The centromeric region where Ryd3 is located suffers suppressed recombination or reduced recombination rate, suggesting potential problems in achieving (1) map-based cloning of Ryd3 and (2) marker selection of the resistance in breeding programmes without the introduction of undesirable traits via linkage drag. [ABSTRACT FROM AUTHOR]

Key message: An insert mutation ofYELLOW -GREEN LEAF2 , encodingHeme Oxygenase 1 , results in significant reduction of its transcript levels, and therefore impairs chlorophyll biosynthesis in rice. Heme oxygenase (HO) in higher plants catalyzes the degradation of heme to synthesize phytochrome precursor and its roles conferring the photoperiodic control of flowering in rice have been revealed. However, its involvement in regulating rice chlorophyll (Chl) synthesis is not fully explored. In this study, we isolated a rice mutant named yellow- green leaf 2 ( ygl2) from a 60Co-irradiated population. Normal grown ygl2 seedlings showed yellow-green leaves with reduced contents of Chl and tetrapyrrole intermediates whereas an increase of Chl a/ b ratio. Ultrastructural analyses demonstrated grana were poorly stacked in ygl2 mutant, resulting in underdevelopment of chloroplasts. The ygl2 locus was mapped to chromosome 6 and isolated via map-based cloning. Sequence analysis indicated that it encodes the rice HO1 and its identity was verified by transgenic complementation test and RNA interference. A 7-Kb insertion was found in the first exon of YGL2/HO1, resulting in significant reduction of YGL2 expressions in the ygl2 mutant. YGL2 was constitutively expressed in a variety of rice tissues with the highest levels in leaves and regulated by temperature. In addition, we found expression levels of some genes associated with Chl biosynthesis and photosynthesis were concurrently altered in ygl2 mutant. These results provide direct evidence that YGL2 has a vital function in rice Chl biosynthesis. [ABSTRACT FROM AUTHOR]

A novel bright-green leaf mutant, bgl11, derived from Nipponbare ( Oryza sativa L. ssp. japonica) treated by ethyl methanesulfonate (EMS), exhibited a distinct bright-green leaf phenotype throughout development. Chlorophyll contents of bgl11 decreased significantly than that of its wild-type parent. Genetic analysis suggested that the bright-green leaf trait was controlled by a single recessive nuclear gene, which was tentatively designed as BGL11( t). To isolate the BGL11( t) gene, a map-based cloning strategy was employed, and the gene was finally mapped in a 94.7 kb region between marker InDel11-5 and InDel11-9 on the long arm of chromosome 11, in which no gene leaded to leaf-color mutation had been mapped or cloned. Cloning and sequencing analysis revealed that, LOC_Os11g38040, which was predicted to encode an expressed protein, had a 9 bp segment deletion in the coding region of bgl11. Furthermore, the transgenic plants with wild-type gene LOC_Os11g38040 were restored to normal phenotype. Accordingly, the gene ( LOC_Os11g38040) was identified as the BGL11( t) gene. These results are very valuable for further study on BGL11( t) gene and illuminating the mechanism of chloroplast development in rice. [ABSTRACT FROM AUTHOR]

Bacterial artificial chromosome (BAC) libraries are widely used in map-based cloning of plant genes. Eastern filbert blight (EFB), caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller, is a devastating disease of European hazelnut ( Corylus avellana L.) in the Pacific Northwest. A dominant allele at a single locus from the obsolete pollenizer 'Gasaway' confers complete resistance. Our map-based cloning efforts use a BAC library for 'Jefferson' hazelnut, which is heterozygous for resistance. Screening the library with primer pairs designed from RAPD markers closely linked to the EFB resistance locus identified 38 BACs. We sequenced 28 of these BACs using Illumina technology, by multiplexing with barcoded adapters. De novo sequence assembly using the programs Velvet and SOPRA and further alignment using CodonCode Aligner generated contigs whose length ranged from 393 to 108,194 bp. The number of contigs per BAC ranged from 1 to 19, and estimated coverage of assembled BACs ranged from 64 % to 100 %. Preliminary analysis of the sequences identified 779 simple sequence repeats (SSRs), from which we developed 23 markers. Of these, 17 were assigned to linkage group 6 adjacent to the disease resistance locus, five were placed on other linkage groups, and one could not be assigned to a linkage group. The BAC sequences and new SSR markers will be useful for our efforts at map-based cloning of the disease resistance gene. [ABSTRACT FROM AUTHOR]

The outgrowth of root hairs from the epidermal cell layer is regulated by a strict genetic regulatory system and external growth conditions. Rice plants cultivated in water-logged paddy land are exposed to a soil ecology that differs from the environment surrounding upland plants, such as Arabidopsis and maize. To identify genes that play important roles in root-hair growth, a forward genetics approach was used to screen for short-root-hair mutants. A short-root-hair mutant was identified, and the gene was isolated using map-based cloning and sequencing. The mutant harbored a point mutation at a splicing acceptor site, which led to truncation of OsFH1 (rice formin homology 1). Subsequent analysis of two additional T-DNA mutants verified that OsFH1 is important for root-hair elongation. Further studies revealed that the action of OsFH1 on root-hair growth is dependent on growth conditions. The mutant Osfh1 exhibited root-hair defects when roots were grown submerged in solution, and mutant roots produced normal root hairs in the air. However, root-hair phenotypes of mutants were not influenced by the external supply of hormones or carbohydrates, a deficiency of nutrients, such as Fe or P, or aeration. This study shows that OsFH1 plays a significant role in root-hair elongation in a growth condition-dependent manner. [ABSTRACT FROM AUTHOR]

The spikelet is a unique structure of grass plants, and its development involved with complicated molecular regulation network. nsg ( nonstop glumes) mutant affecting spikelet development was identified from EMS-treated Jinhui10 ( Oryza sativa L. ssp. indica.). Mutant plants had normal glumes (inner rudimentary glume, empty glumes and lemma/palea) and pedicel at the early flowering stage, but had longer ones at later stage. An extra glume-like organ was found in 84 % of mutant individuals. The number of stamens decreased in most mutant individuals whereas three stigmas or two carpels were found in some mutant individuals. The mutant phenotype suggests that NSG is involved in the whole rice spikelet development. NSG was mapped to a 15 kb region on the chromosome 4. According to sequence analysis, a gene encoding a protein with C2H2 domain exhibited a 13 bp insertion, causing a frame shift in genomics DNA and cDNA in nsg. This gene was identified as the candidated gene of NSG. The mutation of NSG influenced the transcription level of some floral hometic genes. The expression of OsMADS4, OsMADS16, DL and OsMADS3 decreased distinctly, and OsMADS1 increased in nsg panicle, suggests that NSG affected spikelet development through influencing the expression of floral hometic genes. [ABSTRACT FROM AUTHOR]

Key message: Two new alleles of arc3 in Arabidopsis thaliana, arc3-4 and arc3-5, were isolated in the Columbia-0 ecotype. The mutants were characterized in detail using microscopy and molecular techniques. Abstract: Chloroplasts are essential organelles for photosynthesis in plant cells. Division of chloroplasts is coordinated by the internal division machinery (mainly the tubulin-like FtsZ ring) and the external division machinery (mainly the dynamin-like ARC5 ring). Accumulation and replication of chloroplasts3 (ARC3) is important for the correct positioning of chloroplast division machinery. During evolution, ARC3 has probably replaced minicellC (MinC), an important factor involved in positioning of the division site in bacteria. However, the working mechanism of ARC3 is still unclear. Using forward genetic approaches, we isolated two new alleles of arc3 in Arabidopsis thaliana, arc3-4 and arc3-5, in which mutant loci differed from those of previously reported arc3 mutants. Microscopy analyses showed more detailed, and some new, phenotypes of arc3 mutants. Reverse-transcription polymerase chain reaction (RT-PCR) and real-time quantitative RT-PCR (qRT-PCR) results indicated that the mRNA of the ARC3 gene was unstable in arc3-4 and arc3-5 mutant plants. Also, RNA secondary structures of the ARC3 gene were predicted to differ between these two arc3 mutants and wild type. Our studies increase our understanding of the function of ARC3 in chloroplast division. [ABSTRACT FROM AUTHOR]

A floury endosperm mutant, osagpl2-3, was isolated from the M generation of japonica rice cultivar Nipponbare following ethyl methane sulfonate mutagenesis. The osagpl2-3 mutant produced a white-core endosperm compared to the transparent endosperm of the wild type (WT). The results from scanning electron microscope showed that the osagpl2-3 mutant grains comprised of round and loosely packed starch granules, some of which were compounded. The analysis for cooking and nutrition quality traits indicated that the values of gel consistency, gelatinization temperature, and rapid viscosity analysis profile of osagpl2-3 grains were lower than those of the WT. Besides, the protein content, the contents of nine different amino acids, and the thermodynamic parameters of T and Δ T in osagpl2-3 were also different from those of the WT. Genetic analysis revealed that osagpl2-3 mutation was controlled by a single recessive gene. The osagpl2-3 gene was mapped between InDel markers R1M30 and ID1-12 on rice chromosome 1. In the candidate region of the Nipponbare genome, an annotated gene, LOC_Os01g44220 which encodes a large subunit of putative ADP-glucose pyrophosphrylase named OsAPL2 was considered the optimal candidate. Cloning and sequencing of LOC_Os01g44220 in different plants of the osagpl2-3 mutants revealed a single nucleotide mutation (G→A) in the open reading frame region, which led to a substitution of an acidic amino acid Glu (E) by a basic amino acid Lys (K) accordingly. Furthermore, the mutant site is close to the functional domain which interacts with the ADP-Glc. In brief, these results suggested that the osagpl2-3 is a new mutant of OsAPL2. [ABSTRACT FROM AUTHOR]

The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops. [ABSTRACT FROM AUTHOR]

Mi-2 protein, the central component of the NuRD nucleosome remodeling and histone deacetylase complex, plays a role in transcriptional repression in animals. Mi-2-like genes have been reported in Arabidopsis, though their function in monocots remains largely unknown. In the present study, a rice Mi-2-like gene, OsCHR4 ( Oryza sativa Chromatin Remodeling 4, LOC_Os07g03450), was cloned from a rice mutant with adaxial albino leaves. The Oschr4 mutant exhibited defective chloroplasts in adaxial mesophyll, but not in abaxial mesophyll. Ultrastructural observations indicated that proplastid growth and/or thylakoid membrane formation in adaxial mesophyll cells was blocked in the Oschr4 mutant. Subcellular localization revealed that OsCHR4::GFP fusion protein was targeted to the nuclei. OsCHR4 was mainly expressed in the root meristem, flower, vascular bundle, and mesophyll cells by promoter::GUS analysis in transgenic rice. The transcripts of some nuclear- and plastid-encoded genes required for early chloroplast development and photosynthesis were decreased in the adaxial albino mesophyll of the Oschr4 mutant. These observations provide evidence that OsCHR4, the rice Mi-2-like protein, plays an important role in early chloroplast development in adaxial mesophyll cells. The results increase our understanding of the molecular mechanism underlying tissue-specific chloroplast development in plants. [ABSTRACT FROM AUTHOR]

Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences. [ABSTRACT FROM AUTHOR]

A lesion-mimic phenotype in rice ( Oryza sativa L.) spotted leaf 5 ( spl5) indicates that wild-type SPL5 negatively regulates cell death and resistance responses. Previously, the spl5 gene was already mapped to the 80-kb region between two markers SSR7 and RM7121 through a map-based cloning approach. Here, we further showed that the spl5 gene was delimitated into a 15.1-kb genomic region by the high-resolution sequence target site (STS) markers. Subsequent sequencing in this region of spl5 mutant revealed that one candidate gene harbored a single-base deletion, resulting in a frame-shift mutation and a premature stop codon. Bioinformatic analysis showed that SPL5 gene encodes a putative splicing factor 3b subunit 3 (SF3b3) and might be involved in splicing reactions of pre-mature RNAs participating in the regulation of cell death and resistance responses. Further analysis showed that wild-type SPL5 did functionally complement the spl5 phenotype. The data presented here clearly indicate that the SPL5 negatively regulates cell death and resistance responses via modulating RNA splicing in plants. [ABSTRACT FROM AUTHOR]

Three allelic short root mutants were identified by screening mutants with defective root elongation of the rice japonica cultivar Nipponbare mutant library generated via Co γ-ray irradiation mutagenesis. These mutants, designated srt7-1 ( short root 7-1), srt7-2 and srt7-3, respectively, had an extremely short seminal root, adventitious roots and lateral roots. Histological observation revealed the cell length of srt7 mutant roots was significantly shorter than that of wild-type roots. Genetic analysis indicated the short root phenotype was controlled by a single recessive nuclear gene. The SRT7 gene was mapped to a 20-kb interval between the markers STS6 and STS7 on chromosome 4 by a map-based cloning method. Sequencing of the six predicted genes in this region found that all of the three allelic mutants contained a 1-bp or 2-bp deletion in the same gene encoding a putative membrane-bound endo-1,4-β-glucanase. The SRT7 gene was expressed ubiquitously, with higher levels of transcript accumulation in roots at different developmental stages. However, no difference was found in the SRT7 transcription level between the mutant and wild type. Collectively, these results indicate the endo-1,4-β-glucanase encoding gene (LOC_Os04g41970) is likely the candidate for SRT7 that functions posttranscriptionally in rice root elongation. [ABSTRACT FROM AUTHOR]

In rice, the elongated internodes are derived from the vegetative shoot apical meristem (SAM), and the transition of the SAM from the vegetative to the reproductive stage induces internode elongation. In this study, we characterize two shortened uppermost internode mutants ( sui1- 1 and sui1- 2). During the seedling and tillering stages, sui1 plants are morphologically similar to wild-type plants. However, at the heading stage, the sui1- 1 mutant exhibits a shortened uppermost internode and a partly sheathed panicle, and the sui1- 2 mutant shows an extremely shortened uppermost internode and a fully sheathed panicle. Gibberellin treatment results in elongation of every internode, but the shortened uppermost internode phenotype remains unaltered. Microscopic analysis indicates that cell length of sui1- 1 uppermost internode exhibits decreased. Map-based cloning revealed that SUI1 is located on Chromosome 1, and encodes a putative phosphatidyl serine synthase (PSS) family protein. Searches for matches in protein databases showed that OsSUI1 contains the InterPro domain IPR004277, which is conserved in both animal and plant kingdoms. Introduction of a wild-type SUI1 gene fully rescued the mutant phenotype of sui1- 1 and sui1- 2, confirming the identity of the cloned gene. Consistent with these results, the SUI1-RNAi transgenic plants displayed decreased elongation of the uppermost internode. Our results suggest that SUI1 plays an important role in regulating uppermost internode length by decreasing longitudinal cell length in rice. [ABSTRACT FROM AUTHOR]

An es-t ( early senescence-temporary) mutant, produced by ethylene methylsulfonate treatment of strain Nipponbare, was identified in rice. The leaves of es-t appeared yellow at the seedling stage, and had decreased chlorophyll content. Rust spots were found during growth in es-t, especially at the leaf margin and tip. The plants showed a typical early-senescence phenotype at the milky stage. The leaf surface of es-t appeared smoother than wild-type leaves under a scanning electron microscope, because the leaves lack siliceous protuberances around the stoma. Chloroplasts grow abnormally and are filled with many starch grains in es-t. Paraffin section analysis showed that the development of the sclerenchyma cells and vascular bundles were also abnormal in es-t. Genetic analysis indicated that es-t was controlled by a recessive gene, which was finely mapped to a 42-kb interval on chromosome 5. These results will facilitate the positional cloning and functional studies of the gene. [ABSTRACT FROM AUTHOR]

Target leaf spot is one of the major sorghum diseases in southern Japan and caused by a necrotrophic fungus, Bipolaris sorghicola. Sorghum resistance to target leaf spot is controlled by a single recessive gene ( ds1). A high-density genetic map of the ds1 locus was constructed with simple sequence repeat markers using progeny from crosses between a sensitive variety, bmr-6, and a resistant one, SIL-05, which allowed the ds1 gene to be genetically located within a 26-kb region on the short arm of sorghum chromosome 5. The sorghum genome annotation database for BTx623, for which the whole genome sequence was recently published, indicated a candidate gene from the Leucine-Rich Repeat Receptor Kinase family in this region. The candidate protein kinase gene was expressed in susceptible plants but was not expressed or was severely reduced in resistant plants. The expression patterns of ds1 gene and the phenotype of target leaf spot resistance were clearly correlated. Genomic sequences of this region in parental varieties showed a deletion in the promoter region of SIL-05 that could cause reduction of gene expression. We also found two ds1 alleles for resistant phenotypes with a stop codon in the coding region. The results shown here strongly suggest that the loss of function or suppression of the ds1 protein kinase gene leads to resistance to target leaf spot in sorghum. [ABSTRACT FROM AUTHOR]

Resistance to coffee leaf rust is conferred by S3, a major dominant gene that has been introgressed from a wild coffee species Coffea liberica (genome L) into the allotetraploid cultivated species, Coffea arabica (genome CE). As the first step toward the map-based cloning of the S3 gene, using a bacterial artificial chromosome (BAC) library, we describe the construction of a physical map in C. arabica spanning the resistance locus. This physical map consists in two homeologous BAC-contigs of 1,170 and 1,208 kb corresponding to the subgenomes C and E, respectively. Genetic analysis was performed using a single nucleotide polymorphism detection assay based on Sanger sequencing of amplicons. The C. liberica-derived chromosome segment that carries the S3 resistance gene appeared to be introgressed on the sub-genome C. The position of the S3 locus was delimited within an interval of 550 kb on the physical map. In addition, our results indicated a sixfold reduction in recombination frequency in the introgressed S3 region compared to the orthologous region in Coffea canephora. [ABSTRACT FROM AUTHOR]