Disruption of LEAF LESION MIMIC 4 affects ABA synthesis and ROS accumulation in rice

Lesion mimic mutants(LMMs) are advantageous materials for studying programmed cell death(PCD).Although some rice LMM genes have been cloned, the diversity of functions of these genes indicates that the mechanism of cell death regulation in LMMs needs further study. In this study, we identified a rice light-dependent leaf lesion mimic mutant 4(llm4) that showed abnormal chloroplast structure, photoinhibition, reduced photosynthetic protein levels, massive accumulation of reactive oxygen species(ROS), and PCD. Map-based cloning and complementation testing revealed that LLM4 encodes zeaxanthin epoxidase(ZEP), an enzyme involved in the xanthophyll cycle, which functions in plant photoprotection,ROS scavenging, and carotenoid and abscisic acid(ABA) biosynthesis. The ABA content was decreased,and the contents of 24 carotenoids differed between the llm4 mutant and the wild type(WT). The llm4mutant showed reduced dormancy and greater sensitive to ABA than the WT. We concluded that the mutation of LLM4 resulted in the failure of xanthophyll cycle, in turn causing ROS accumulation. The excessive ROS accumulation damaged chloroplast structure and induced PCD, leading eventually to the formation of lesion mimics.

Identification of key genes involved in flavonoid and terpenoid biosynthesis and the pathway of triterpenoid biosynthesis in Passiflora edulis

Passion fruit(Passiflora edulis Sims) is a vine of the Passiflora genus in the Passifloraceae family. The extracted components include flavonoids and terpenoids, which have good anti-anxiety and anti-inflammatory effects in humans.In this study, we analyzed the transcriptomes of four tissues of the ‘Zixiang’ cultivar using RNA-Seq, which provided a dataset for functional gene mining. The de novo assembly of these reads generated 96 883 unigenes, among which 61 022 unigenes were annotated(62.99% yield). In addition to its edible value, another important application of passion fruit is its medicinal value. The flavonoids and terpenoids are mainly derivatives of luteolin, apigenin, cycloartane triterpenoid saponins and other active substances in leaf extracts. A series of candidate unigenes in the transcriptome data that are potentially involved in the flavonoid and terpenoid synthesis pathways were screened using homologybased BLAST and phylogenetic analysis. The results showed that the biosynthesis of triterpenoids in passion fruit comes from the branches of the mevalonate(MVA) and 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate(MEP/DOXP) pathways, which is different from the MVA pathway that is used in other fruit trees. Most of the candidate genes were found to be highly expressed in the leaves and/or flowers. Quantitative real-time PCR(qRT-PCR) verification was carried out and confirmed the reliability of the RNA-Seq data. Further amplification and functional analysis of these putative unigenes will provide additional insight into the biosynthesis of flavonoids and terpenoids in passion fruit.

Development and Identification of Introgression Lines from Cross of Oryza sativa and Oryza minuta

Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines（ILs）,which derived from an accession of Oryza minuta（accession No.101133） with BBCC genome,as the donor,and an elite indica cultivar IR24（O.sativa）,as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat（SSR） markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64% of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5% 25.2%,with an average of 8.3%.Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.

Rapid gene expression change in a novel synthesized allopolyploid population of cultivated peanut×Arachis doigoi cross by cDNA-SCoT and HFO-TAG technique

AIIopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and （or） polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species. To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA start codon targeted polymorphism （cDNA-SCoT） and cDNA high-frequency oligonucleotide-targeting active gene （cDNA-HFO-TAG） techniques, from the hybrids （F1） and newly synthesized allopolyploid generations （S0-$3） between tetraploid cultivated peanut Zhongkaihua 4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the FI hybrid or immediately after chromosome doubling. Three types of gene expression changes were observed, including complete silence （gene from progenitors was not expressed in all progenies）, incomplete silence （gene expressed only in some progenies） and new genes activation. Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions. The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG. These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments （TDFs） probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to thwe genetic diploidization of newly formed allopolyploids. Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.

Assessment of the Genetic Relationship and Diversity of Mango and Its Relatives by cpISSR Marker

Chloroplast inter-simple sequence repeat markers in mango were developed and used to analyze the genetic relationship and diversity of mango and its relatives. Thirty-six mango cultivars （Mangifera indica L.） and its relative species collected from the fruit germplasm collection in the Guangxi Academy of Agricultural Sciences, China, were examined by ISSR-PCR with chloroplast DNA （cpDNA）. Eight better primers for chloroplast DNA that provided reproducible, polymorphic DNA amplification patterns were screened from 50 ISSR primers and used for UPGMA analysis. According to the band patterns with 8 primers for chloroplast DNA, all cultivars tested were distinguished from each other and these showed ample genetic diversity; the average percentage of polymorphism was 77.2%. The 36 samples could be clustered into four groups by UPGMA analysis at the coefficient 0.74. The results indicated that the cplSSR marker was a new powerful tool for the identification of mango cultivars or its relative species, and their genetic relationship analysis and diversity evaluation.

Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea （cultivated peanut） from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut （A. hypogaea L.） varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut （A. hypogaea L.） and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

Effect of Gibberellin,Light and Genotype on Somatic Embryogenesis and Plantlet Regeneration of Peanut

[ Objective] Peanut in vitro regeneration system was optimized to provide technical support for its genetic transformation and mutagenesis. [ Method ] The effect of gibberellin, light and genotype on somatic embryogenesis and plantiet regeneration of peanut was studied using Guihua peanut cuhivar as materials, leallets as explants, MS ＋ 10 mg/L 2, 4-D as somatic embryo induction medium, and MS ＋3 mg/L 6-BA ＋0. 8 mg/L NAA ＋ （0 - 15 mg/L） GA3 as plantlet induction me- dium. [Result]The somatic embryo induction rate of five peanut varieties under light condition of light： dark = 14 h： 10 h was significantly higher compared with that under dark condition by 7, 5 - 37.5 percent points. Among different peanut varieties, Guihua 26 represented the highest somatic embryo induction rate of 62. 8%, while Guihua 833 represented the lowest somatic embryo induction rate of 21.7%. Adding 5 - 15 mg/LGA3 in plantlet induction medium was conducive to improving the induction rate of plandets derived from somatic embryos. With addition of 5 mg/L GA3, Guihua 26 and Guihna 771 represented the highest plantlet induction rate of 42.8% and 35.3%, respectively; with addition of 15 mg/L GA3, Guihua 836, Guihua 1026 and Guihna 833 represented the highest plantlet in- duction rate of 38.7%, 33.3% and 26.4L%, respectively. Among different combinations of peanut variety and GA3 concentration, plantlet induction rate reached the highest in the combination Guihua 26 ＋ 5 mg/L CA.3 arid reached the lowest in the combination Guihua 836 ＋ 15 mg/L GA3. [ Conclusion] Appropriate light conditions are conducive to peanut somatic embryogenesis in vitro. Adding GA3 in plantlet induction medium is conducive to promoting plantlet regeneration. Guihua 26 and Guihua 836 are the best peanut varieties among the experimental genotypes for somatic embryogenesis and plant regeneration.

Identification of a Resistance Gene bls1 to Bacterial Leaf Streak in Wild Rice Oryza rufipogon Griff

Bacterial leaf streak （BLS） of rice, caused by Xanthomonas oryzae pv. oryzicola （Xoc） is a worldwide destructive disease. Development of resistant varieties is considered to be one of the most effective and eco-friendly ways to control the disease. However, only a few genes/QTLs having resistance to BLS have been identified in rice until now. In the present study, we have identified and primarily mapped a BLS-resistance gene, blsl, from a rice line DP3, derived from the wild rice species Oryza rufipogon Griff. A BC2F2 （9311/DP3//9311） population was constructed to map BLS-resistance gene in the rice line DP3. The segregation of the resistant and susceptible plants in BCzFz in 1：3 ratio （Z2=0.009, Z20 05,1=3.84, P〉0.05）, suggested that a recessive gene confers BLS resistance in DP3. In bulked segregant analysis （BSA）, two SSR markers RM8116 and RM584 were identified to be polymorphic in resistant and susceptible DNA bulks. For further mapping the resistance gene, six polymorphic markers around the target region were applied to analyze the genotypes of the BC2F2 individuals. As a result, the BLS-resistant gene, designated as blsl, was mapped in a 4.0-cM region flanked by RM587 and RM510 on chromosome 6.

The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era

Next-generation sequencing technological advances,affording high-throughput,scalable,and fast assemblies,have enabled genome editing techniques that allow us to remove,insert,and modify genes for rapid and precise functional investigations.

Retraction of: A calreticulin/gC1qRcomplex prevents cells from dying: a conserved mechanism from arthropods to humans

This paper(J.Mol.Cell Biol.(2013),5(2),120–131;doi:10.1093/jmcb/mjt005),together with its corrigendum(J.Mol.Cell Biol.(2014),6(6):535–536;doi:10.1093/jmcb/mju043)have been retracted by the three last authors andthe journal’s Editor-in-Chief due to inaccuratefigure handling and assembly made by the first author ApiruckWatthanasurorot.The first author has admitted responsibility for these anomalies.The authors apologize to the readers and editors of J.Mol.Cell Biol.for any inconvenience caused.