Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
Miscanthus lutarioriparius is an endemic species that grows along the middle and lower reaches of the Yangtze River and is a valuable source of germplasm for the development of second-generation energy crops. The plant that propagates via seeds, stem nodes, and rhizomes shows high phenotypic variation and strong local adaptation. Here, we examined the magnitude and spatial distribution of genetic variation in M. lutarioriparius across its entire distributional range and tested underlying factors that shaped its genetic variation. Population genetic analyses were conducted on 644 individuals from 25 populations using 16 microsatellite markers. M. lutarioriparius exhibited a high level of genetic variation (HE = 0.682–0.786; Ar = 4.74–8.06) and a low differentiation (FST = 0.063; Dest = 0.153). Of the total genetic variation, 10% was attributed to the differences among populations (df = 24, P < 0.0001), whereas 90% was attributed to the differences among individuals (df = 619, P ≤ 0.0001). Genetic diversity did not differ significantly across longitudes and did not increase in the populations growing downstream of the Yangtze River. However, significant associations were found between genetic differentiation and spatial distance. Six genetic discontinuities were identified, which mostly distributed among downstream populations. We conclude that anthropogenic factors and landscape features both contributed to shaping the pattern of gene flow in M. lutarioriparius, including long-distance bidirectional dispersal. Our results explain the genetic basis of the high degree of adaptability in M. lutarioriparius and identify potential sources of new germplasm for the domestication of this potential second-generation energy crop.
Peer Review Status:
Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Lijuan Wei
Hongju Jian
Kun Lu
Fiona Filardo
Nengwen Yin
Liezhao Liu
Cunmin Qu
Wei Li
Hai Du
Jiana Li
Abstract：
Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Anna Plasencia
Marçal Soler
Annabelle Dupas
Nathalie Ladouce
Guilherme Silva-Martins
Yves Martinez
Catherine Lapierre
Claudine Franche
Isabelle Truchet
Jacqueline Grima-Pettenati
Abstract：
Eucalyptus are of tremendous economic importance being the most planted hardwoods worldwide for pulp and paper, timber and bioenergy. The recent release of the Eucalyptus grandis genome sequence pointed out many new candidate genes potentially involved in secondary growth, wood formation or lineage-specific biosynthetic pathways. Their functional characterization is, however, hindered by the tedious, time-consuming and inefficient transformation systems available hitherto for eucalypts. To overcome this limitation, we developed a fast, reliable and efficient protocol to obtain and easily detect co-transformed E. grandis hairy roots using fluorescent markers, with an average efficiency of 62%. We set up conditions both to cultivate excised roots in vitro and to harden composite plants and verified that hairy root morphology and vascular system anatomy were similar to wild-type ones. We further demonstrated that co-transformed hairy roots are suitable for medium-throughput functional studies enabling, for instance, protein subcellular localization, gene expression patterns through RT-qPCR and promoter expression, as well as the modulation of endogenous gene expression. Down-regulation of the Eucalyptus cinnamoyl-CoA reductase1 (EgCCR1) gene, encoding a key enzyme in lignin biosynthesis, led to transgenic roots with reduced lignin levels and thinner cell walls. This gene was used as a proof of concept to demonstrate that the function of genes involved in secondary cell wall biosynthesis and wood formation can be elucidated in transgenic hairy roots using histochemical, transcriptomic and biochemical approaches. The method described here is timely because it will accelerate gene mining of the genome for both basic research and industry purposes.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Xun Wu
Yongxiang Li
Yunsu Shi
Yanchun Song
Dengfeng Zhang
Chunhui Li
Edward S. Buckler
Yu Li
Zhiwu Zhang
Tianyu Wang
Abstract：
Both insufficient and excessive male inflorescence size leads to a reduction in maize yield. Knowledge of the genetic architecture of male inflorescence is essential to achieve the optimum inflorescence size for maize breeding. In this study, we used approximately eight thousand inbreds, including both linkage populations and association populations, to dissect the genetic architecture of male inflorescence. The linkage populations include 25 families developed in the U.S. and 11 families developed in China. Each family contains approximately 200 recombinant inbred lines (RILs). The association populations include approximately 1000 diverse lines from the U.S. and China. All inbreds were genotyped by either sequencing or microarray. Inflorescence size was measured as the tassel primary branch number (TBN) and tassel length (TL). A total of 125 quantitative trait loci (QTLs) were identified (63 for TBN, 62 for TL) through linkage analyses. In addition, 965 quantitative trait nucleotides (QTNs) were identified through genomewide study (GWAS) at a bootstrap posterior probability (BPP) above a 5% threshold. These QTLs/QTNs include 24 known genes that were cloned using mutants, for example Ramosa3 (ra3), Thick tassel dwarf1 (td1), tasselseed2 (ts2), liguleless2 (lg2), ramosa1 (ra1), barren stalk1 (ba1), branch silkless1 (bd1) and tasselseed6 (ts6). The newly identified genes encode a zinc transporter (e.g. GRMZM5G838098 and GRMZM2G047762), the adapt in terminal region protein (e.g. GRMZM5G885628), O-methyl-transferase (e.g. GRMZM2G147491), helix-loop-helix (HLH) DNA-binding proteins (e.g. GRMZM2G414252 and GRMZM2G042895) and an SBP-box protein (e.g. GRMZM2G058588). These results provide extensive genetic information to dissect the genetic architecture of inflorescence size for the improvement of maize yield.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
Fe deficiency is a widespread nutritional disorder in plants. The basic helix-loop-helix (bHLH) transcription factors (TFs), especially Ib subgroup bHLH TFs which are involved in iron uptake, have been identified. In this study, an IVc subgroup bHLH TF MdbHLH104 was identified and characterized as a key component in the response to Fe deficiency in apple. The overexpression of the MdbHLH104 gene noticeably increased the H+-ATPase activity under iron limitation conditions and the tolerance to Fe deficiency in transgenic apple plants and calli. Further investigation showed that MdbHLH104 proteins bonded directly to the promoter of the MdAHA8 gene, thereby positively regulating its expression, the plasma membrane (PM) H+-ATPase activity and Fe uptake. Similarly, MdbHLH104 directly modulated the expression of three Fe-responsive bHLH genes, MdbHLH38, MdbHLH39 and MdPYE. In addition, MdbHLH104 interacted with 5 other IVc subgroup bHLH proteins to coregulate the expression of the MdAHA8 gene, the activity of PM H+-ATPase and the content of Fe in apple calli. Therefore, MdbHLH104 acts together with other apple bHLH TFs to regulate Fe uptake by modulating the expression of the MdAHA8 gene and the activity of PM H+-ATPase in apple.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Gaurav Agarwal
Vanika Garg
Himabindu Kudapa
Dadakhalandar Doddamani
Lekha T. Pazhamala
Aamir W. Khan
Mahendar Thudi
Suk-Ha Lee
Rajeev K. Varshney
Abstract：
APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Xiaojiao Han
Hengfu Yin
Xixi Song
Yunxing Zhang
Mingying Liu
Jiang Sang
Jing jiang
Jihong Li
Renying Zhuo
Abstract：
The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Sebastian Beier
Axel Himmelbach
Thomas Schmutzer
Marius Felder
Stefan Taudien
Klaus F. X. Mayer
Matthias Platzer
Nils Stein
Uwe Scholz
Martin Mascher
Abstract：
Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
Switchgrass (Panicum virgatum L.) is considered a model herbaceous energy crop for the USA, for its adaptation to marginal land, low rainfall and nutrient-deficient soils; however, its low biomass yield is one of several constraints, and this might be rectified by modulating plant growth regulator levels. In this study, we have determined whether the expression of the Zea mays gibberellin 20-oxidase (ZmGA20ox) cDNA in switchgrass will improve biomass production. The ZmGA20ox gene was placed under the control of constitutive CaMV35S promoter with a strong TMV omega enhancer, and introduced into switchgrass via Agrobacterium-mediated transformation. The transgene integration and expression levels of ZmGA20ox in T0 plants were analysed using Southern blot and qRT-PCR. Under glasshouse conditions, selected transgenic plants exhibited longer leaves, internodes and tillers, which resulted in twofold increased biomass. These phenotypic alterations correlated with the levels of transgene expression and the particular gibberellin content. Expression of ZmGA20ox also affected the expression of genes coding for key enzymes in lignin biosynthesis. Our results suggest that the employment of ectopic ZmGA20ox and selection for natural variants with high level expression of endogenous GA20ox are appropriate approaches to increase biomass production of switchgrass and other monocot biofuel crops.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Helena Sta?ková
Alex R. Hastie
Saki Chan
Jan Vrána
Zuzana Tulpová
Marie Kubaláková
Paul Visendi
Satomi Hayashi
Mingcheng Luo
Jacqueline Batley
David Edwards
Jaroslav Doleel
Hana imková
Abstract：
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight-parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high-marker-density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
OsSPX1, a rice SPX domain gene, involved in the phosphate (Pi)-sensing mechanism plays an essential role in the Pi-signalling network through interaction with OsPHR2. In this study, we focused on the potential function of OsSPX1 during rice reproductive phase. Based on investigation of OsSPX1 antisense and sense transgenic rice lines in the paddy fields, we discovered that the down-regulation of OsSPX1 caused reduction of seed-setting rate and filled grain number. Through examination of anthers and pollens of the transgenic and wild-type plants by microscopy, we found that the antisense of OsSPX1 gene led to semi-male sterility, with lacking of mature pollen grains and phenotypes with a disordered surface of anthers and pollens. We further conducted rice whole-genome GeneChip analysis to elucidate the possible molecular mechanism underlying why the down-regulation of OsSPX1 caused deficiencies in anthers and pollens and lower seed-setting rate in rice. The down-regulation of OsSPX1 significantly affected expression of genes involved in carbohydrate metabolism and sugar transport, anther development, cell cycle, etc. These genes may be related to pollen fertility and male gametophyte development. Our study demonstrated that down-regulation of OsSPX1 disrupted rice normal anther and pollen development by affecting carbohydrate metabolism and sugar transport, leading to semi-male sterility, and ultimately resulted in low seed-setting rate and grain yield.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Abstract：
Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Chouaib Meziadi
Sophie Blanchet
Manon M.S. Richard
Marie-Laure Pilet-Nayel
Valérie Geffroy
Stéphanie Pflieger
Abstract：
Pea (Pisum sativum L.) is an important legume worldwide. The importance of pea in arable rotations and nutritional value for both human and animal consumption have fostered sustained production and different studies to improve agronomic traits of interest. Moreover, complete sequencing of the pea genome is currently underway and will lead to the identification of a large number of genes potentially associated with important agronomic traits. Because stable genetic transformation is laborious for pea, virus-induced gene silencing (VIGS) appears as a powerful alternative technology for determining the function of unknown genes. In this work, we present a rapid and efficient viral inoculation method using DNA infectious plasmids of Bean pod mottle virus (BPMV)-derived VIGS vector. Six pea genotypes with important genes controlling biotic and/or abiotic stresses were found susceptible to BPMV carrying a GFP reporter gene and showed fluorescence in both shoots and roots. In a second step, we investigated 37 additional pea genotypes and found that 30 were susceptible to BPMV and only 7 were resistant. The capacity of BPMV to induce silencing of endogenes was investigated in the most susceptible genotype using two visual reporter genes: PsPDS and PsKORRIGAN1 (PsKOR1) encoding PHYTOENE DESATURASE and a 1,4-β-D-glucanase, respectively. The features of the ‘one-step’ BPMV-derived VIGS vector include (i) the ease of rub-inoculation, without any need for biolistic or agro-inoculation procedures, (ii) simple cost-effective procedure and (iii) noninterference of viral symptoms with silencing. These features make BPMV the most adapted VIGS vector in pea to make low- to high-throughput VIGS studies.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-04
Filippo M. Bassi
Farhad Ghavami
Matthew J. Hayden
Yi Wang
Kerrie L. Forrest
Stephan Kong
Rhoderissa Dizon
Monika K. Michalak de Jimenez
Steven W. Meinhardt
Mohamed Mergoum
Yong Q. Gu
Shahryar F. Kianian
Abstract：
The nuclear-encoded species cytoplasm specific (scs) genes control nuclear–cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear–cytoplasmic compatibility in wheat.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-03
Abstract：
Plant engineered to express double-stranded RNA (dsRNA) can target the herbivorous insect gene for silencing. Although mounting evidence has emerged to support feasibility of this new pest control technology, field application is slow largely due to lack of potent targets. Here, we show that suppression of the gene encoding NDUFV2, a subunit of mitochondrial complex I that catalyses NADH dehydrogenation in respiratory chain, was highly lethal to insects. Feeding cotton bollworm (Helicoverpa armigera) larvae with transgenic cotton tissues expressing NDUFV2 dsRNA led to mortality up to 80% within 5 days, and almost no larvae survived after 7 days of feeding, due to the altered mitochondrial structure and activity. Transcriptome comparisons showed a drastic repression of dopa decarboxylase genes. Reciprocal assays with Asian corn borer (Ostrinia furnacalis), another lepidopteran species, revealed the sequence-specific effect of NDUFV2 suppression. Furthermore, the hemipteran lugus Apolygus lucorum was also liable to NDUFV2 repression. These data demonstrate that the mitochondrial complex I is a promising target with both sequence specificity and wide applicability for the development of new-generation insect-proof crops.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-03
Abstract：
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-03
Abstract：
Rice caryopsis as one of the most important food sources for humans has a complex structure that is composed of maternal tissues including the pericarp and testa and filial tissues including the endosperm and embryo. Although rice caryopsis studies have been conducted previously, a systematic characterization throughout the entire developmental process is still lacking. In this study, detailed morphological examinations of caryopses were made during the entire 30-day developmental process. We observed some rapid changes in cell differentiation events and cataloged how cellular degeneration processes occurred in maternal tissues. The differentiations of tube cells and cross cells were achieved by 9 days after pollination (DAP). In the testa, the outer integument was degenerated by 3 DAP, while the outer layer of the inner integument degenerated by 7 DAP. In the nucellus, all tissues with the exception of the nucellar projection and the nucellar epidermis degenerated in the first 5 DAP. By 21 DAP, all maternal tissues, including vascular bundles, the nucellar projection and the nucellar epidermal cells were degenerated. In summary, this study provides a complete atlas of the dynamic changes in cell differentiation and degeneration for individual maternal cell layers of rice caryopsis.
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-03
Yan Zou
Satya Chintamanani
Ping He
Hirotada Fukushige
Liping Yu
Meiyu Shao
Lihuang Zhu
David F. Hildebrand
Xiaoyan Tang
Jian-Min Zhou
Abstract： Jasmonates (JAs) are rapidly induced after wounding and act as key regulators for wound induced signaling pathway. However, what perceives the wound signal and how that triggers JA biosynthesis remains poorly understood. To identify components involved in Arabidopsis wound and JA signaling pathway, we screened for mutants with abnormal expression of a luciferase reporter, which is under the control of a wound-responsive promoter of an ethylene response factor (ERF) transcription factor gene, RAP2.6 (Related to APetala 2.6). The rea1 (R
Peer Review Status:Awaiting Review
Subjects: Biology >> Botany >> Plant cytology, plant genetics & plant morphology submitted time 2016-05-03
Abstract： Due to the remarkable adaptability to various environments, rice varieties with diverse flowering times have been domesticated or improved from Oryza rufipogon. Detailed knowledge of the genetic factors controlling flowering time will facilitate understanding the adaptation mechanism in cultivated rice and enable breeders to design appropriate genotypes for distinct preferences. In this study, four genes (Hd1, DTH8, Ghd7 and OsPRR37) in a rice long-day suppression pathway were collected and sequenced in 154, 74, 69 and 62 varieties of cultivated rice (Oryza sativa) respectively. Under long-day conditions, varieties with nonfunctional alleles flowered significantly earlier than those with functional alleles. However, the four genes have different genetic effects in the regulation of flowering time: Hd1 and OsPRR37 are major genes that generally regulate rice flowering time for all varieties, while DTH8 and Ghd7 only regulate regional rice varieties. Geographic analysis and network studies suggested that the nonfunctional alleles of these suppression loci with regional adaptability were derived recently and independently. Alleles with regional adaptability should be taken into consideration for genetic improvement. The rich genetic variations in these four genes, which adapt rice to different environments, provide the flexibility needed for breeding rice varieties with diverse flowering times.
Peer Review Status:Awaiting Review
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