Genetic Analysis of Stripe Disease Resistance in Rice Restorer Line C224 Using Major Gene plus Polygene Mixed Effect Model

The inheritance of stripe disease resistance in a rice restorer line C224 was analyzed using the mixed effect model of major gene plus polygene for quantitative traits.In addition,the resistance was investigated in seven crosses of C224 with maintainer lines.The results showed that the stripe resistance of C224 was controlled by two major genes with additive-dominance-epistasis effects plus polygenes with additive-dominance effects （E-1 model）.These two genes had additive effects of-12.47% and-24.75%,respectively,showing negative dominance effects.There were significant epistasis and interaction effects between the two major genes.The heritability of the two major genes was 92.12%,while that of polygenes was 2.74%,indicating that the stripe resistance had dominant major gene effect.Of the seven crosses,five displayed high or medium resistance to the stripe disease.

Genetic Variants in the ELOVL5 but not ELOVL2 Gene Associated with Polyunsaturated Fatty Acids in Han Chinese Breast Milk

The present study was designed to examine the contributions of the fatty acid elongase （ELOVL） gene polymorphisms to the levels of polyunsaturated fatty acids （PUFAs） in breast milk. Two hundred and nine healthy Han Chinese mothers were included in the study. Carriers of minor alleles of SNPs （rs2397142 and rs9357760） in ELOVL5 were associated with higher levels of linoleic acid （LA）, dihomo-γ-linolenic acid （DGLA）, arachidonic acid （AA）, docosatetraenoic acid （DTA）, docosahexenoic acid （DHA）, while in rs209512 of ELOVL5 the carriers of minor alleles had lower levels of DTA compared to major homozygote alleles （P ranged from 0.004-0.046）, and genetically explained variability ranged from 3.2% for eicosapentaenoic acid （EPA） to 6.0% for LA. Our findings demonstrated that common variation in ELOVL5 gene encoding rate-limiting enzymes in the metabolism of PUFAs contribute to the PUFAs in breast milk.

Cloning and genetic transformation of a novel rice gene OsAPT2

A novel rice gene OsAPT2,which encodes a putative adenine phosphoribosyl transferase(APRT),was cloned.Its full-length cDNA is 1125bp,composing an ORF encoding 212 amino acid residues and a stop cordon,a 5' UTR of 123 bp and a 3' UTR of 363 bp.The sequence data have been submitted to the DDBJ/EMBL/GenBank databases(accession number:AY238894).The deduced amino acid sequence of OsAPT2 is highly homologous to those of previously reported APRTs.The genomic OsAPT2 gene contains 7 exons and 6 introns.Its total length is 4758 bp.Then,an antisense expression vector of the full-length OsAPT2 cDNA was constructed and transformed into rice variety Taibei309 by Agrobacterium tumefaciens mediated transformation method.In total,650 T0 transgenic plants were obtained based on both antibiotic screening and specific PCR identification.One hundred individuals of them were selected and planted in Hainan Island.From those 11 male sterile lines with seed-setting rate lower than 3% in bagged spike were obtained.Results suggest that OsAPT2 is involved in male sterility.Nine of the 11 male sterile lines were constitutive sterile lines;two of the 11 male sterile lines were thermo-sensitive genic male sterile lines,which may be useful in hybride rice breeding.

Genetics and Expression of the Brown Lint Gene in Colored Cotton

The major cotton grown commercially in the world is white lint,but recently many people prefer to have garments made by natural colored cotton.This can be used directly in textile industries,avoiding the complicated and unsafe processes of bleaching and dying,and thus it is eco-friendly.However,little is known about the heredity of the colored lint gene in colored cotton.In the present study,

Genetic difference of Chinese horseshoe crab(Tachypleus tridentatus) in southeast coast of China based on mitochondrial COI gene analysis

Population genetic structure and historical demography of Chinese horseshoe crab (T.tridentatus)along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit Ⅰ (COI) fragment.The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities:Ninghai in Zhejiang Province,Meizhou and Zhangpu in Fujian Province,Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province.Sequence variation was relatively low with a total of seven transitions observed.In all localities,Haplotype H3 was the dominant type observed among eight haplotypes defined previously,and was at the center of radiation in Median-Joining network.The prolonged star-like network suggests a signature of population expansions.The level of diversity was low in total,with haplotype diversity ( Hd) being equal to 0.765 and nucleotide diversity (π) being equal to 0.00118,respectively.The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations.Both mismatch distribution analysis and Fu's Fs test provided consistent inference of historic population expansion.The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.

The Genetic Structure and Diversity of Repomucenus curvicornis Inhabiting Liaoning Coast Based on Mitochondrial COⅠ Gene and Control Region

[Object] This study was conducted to explore the genetic diversity and structure of the wild Repomucenus curvicornis inhabiting Liaoning Coast, China. [Method] The mitochondrial COⅠ gene and control region（CR） were PCR amplified from the wild R. curvicornis populations from the Liaodong Bay（n=22） and the northern Yellow Sea（n=18）, sequenced and analyzed for genetic diversity. [Result] The contents of A, T, C and G of 624 bp COⅠ gene were 24.09%, 31.04%, 25.28%, and 19.59%, and those of 460 bp CR fragment were 32.96%, 32.80%, 14.86% and 19.38%, respectively. The total number of variable sites, average number of nucleotide differences（ k）, haplotype diversity（H） and nucleotide diversity（π） based on COⅠ gene were 38, 4.67,（0.96±0.02） and（0.007 5±0.004 2）, and those based on CR fragment were 26, 3.35,（0.97 ±0.02） and（0.007 3±0.004 3）, respectively. Based on mitochondrial COⅠ gene and CR, the genetic diversity of Liaodong Bay population was lower than that of the northern Yellow Sea population. The AMOVA analysis based on CR fragments revealed almost significant genetic divergence between the Liaodong Bay and the northern Yellow Sea populations, while there was no significant genetic divergence based on COⅠ gene. The results showed that CR and COⅠ gene are effective molecular markers for detecting the genetic diversity of R. curvicornis population, while CR is more reliable than COⅠ gene in detecting the genetic structure. [Conclusion] CR is an appropriate marker for genetic analysis of marine fish population.

Genetic expression and effects of the rolled leaf gene Rl(t) in hybrid rice (Oryza sativa L.)

We constructed a nearisogenic line of rolled leaf gene Rl(t), which ex-pressed incompletely dondnance for the character of rolled leaf(RL), with ge-netic background of Zhenshan 97B. Using RL Zhenshan 97B and the originalZhenshan 97B as the female parents, and Minghui 63 and Yanhui 559 as themale parents, crosses of RL Shanyu 63 (RS63) and Shanyu 63(S63), RLShanyou 559 (RS559) and Shanyou 559 (S559) were made. Inheritance andeffects of Rl(t) in hybrid rice were studied at the flowering and at the 20 d afterflowering, respectively. Results were as follow:

Fertility Expression of TGMS-Genes in the Backgrounds of indica CMS-lines,B-lines and R-lines of Hybrid Rice

The generation fertility of 51 F1, 19 F2 and 6 BC1 between 3 thermo-sensitive genic male sterile lines （TGMS-lines） Pei＇ai 64S, 6311S and 360S, and the three lines of hybrid rice including 7 indica cytoplasmic male sterile lines （CMS-lines） and their corresponding maintainer lines （B-lines） and 3 indica restorer lines （R-lines） were investigated to study the expression of TGMS-genes in the backgrounds of the three lines of hybrid rice. Pei＇ai 64S has stronger fertility restoring （Rf） genes for CMS-lines and its TGMS trait is governed by 2 pairs of independent recessive genes; The TGMS trait of 6311S is governed by a single recessive gene with weaker Rf-gene in 6311S and the TGMS trait of 360S is governed by a single recessive gene with no Rf-gene in 360S. The investigation on the fertility of F1 plants between 5 CMS-lines and 4 TGMS generations selected from F2 plants of 4 CMS-lines x 6311S confirmed that the expression of TGMS-gene was controlled by Rf-gene in the genetic background of cytoplasm of CMS-lines, but not affected by Rf-gene in the genetic background of normal fertile cytoplasm. The potential breeding strategies of TGMS-lines with cytoplasm of CMS-lines and CMS-lines with the nucleus of TGMS-genes were discussed.

Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng on Wheat Chromosome 6D

Stripe rust （yellow rust）, caused by Puccinia striiformis f. sp. tritici （Pst）, is one of the most devastating diseases of wheat throughout the world. H9020-1-6-8-3 is a translocation line originally developed from interspeciifc hybridization between wheat line 7182 and Psathyrostachys huashanica Keng and is resistant to most Pst races in China. To identify the resistance gene（s） in the translocation line, H9020-1-6-8-3 was crossed with susceptible cultivar Mingxian 169, and seedlings of the parents, F1, F2, F3, and BC1 generations were tested with prevalent Chinese Pst race CYR32 under controlled greenhouse conditions. The results indicated that there is a single dominant gene, temporarily designated as YrH9020a, conferring resistance to CYR32. The resistance gene was mapped by the F2 population from Mingxian 169/H9020-1-6-8-3. It was linked to six microsatellite markers, including Xbarc196, Xbarc202, Xbarc96, Xgpw4372, Xbarc21, and Xgdm141, lfanked by Xbarc96 and Xbarc202 with at 4.5 and 8.3 cM, respectively. Based on the chromosomal locations of these markers and the test of Chinese Spring （CS） nullitetrasomic and ditelosomic lines, the gene was assigned to chromosome 6D. According to the origin and the chromosomal location, YrH9020a might be a new resistance gene to stripe rust. The lfanking markers linked to YrH9020a could be useful for marker-assisted selection in breeding programs.

DCDC2 gene polymorphisms are associated with developmental dyslexia in Chinese Uyghur children

Developmental dyslexia is a complex reading and writing disorder with strong genetic components. In previous genetic studies about dyslexia, a number of candidate genes have been identified. These include DCDC2, which has repeatedly been associated with developmental dyslexia in various European and American populations. However, data regarding this relationship are varied according to population. The Uyghur people of China represent a Eurasian population with an interesting genetic profile. Thus, this group may provide useful information about the association between DCDC2 gene polymorphisms and dyslexia. In the current study, we examined genetic data from 392 Uyghur children aged 8–12 years old from the Xinjiang Uyghur Autonomous Region of China. Participants included 196 children with dyslexia and 196 grade-, age-, and gender-matched controls. DNA was isolated from oral mucosal cell samples and fourteen single nucleotide polymorphisms（rs6456593, rs1419228, rs34647318, rs9467075, rs793862, rs9295619, rs807701, rs807724, rs2274305, rs7765678, rs4599626, rs6922023, rs3765502, and rs1087266） in DCDC2 were screened via the SNPscan method. We compared SNP frequencies in five models（Codominant, Dominant, Recessive, Heterozygote advantage, and Allele） between the two groups by means of the chi-squared test. A single-locus analysis indicated that, with regard to the allele frequency of these polymorphisms, three SNPs（rs807724, rs2274305, and rs4599626） were associated with dyslexia. rs9467075 and rs2274305 displayed significant associations with developmental dyslexia under the dominant model. rs6456593 and rs6922023 were significantly associated with developmental dyslexia under the dominant model and in the heterozygous genotype. Additionally, we discovered that the T-G-C-T of the four-marker haplotype（rs9295619-rs807701-rs807724-rs2274305） and the T-A of the two-marker haplotype（rs3765502-1087266） were significantly different between cases and controls. Thus, we conclude that DCDC2 gene polymorphisms are associated with developmental dyslexia in Chinese Uyghur children.

Enhanced resistance to Botrytis cinerea and Rhizoctonia solani in transgenic broccoli with a Trichoderma viride endochitinase gene

A endochitinase gene（Tch） from the fungus Trichoderma viride was introduced into broccoli（Brassica oleracea var. italica） by Agrobacterium-mediated transformation. Sixty-eight putative transformants were obtained and the presence of the Tch gene was confirmed by both PCR and Southern blot analysis. RT-PCR analysis showed an accumulation of the transcript encoding the endochitinase protein in the transgenic plants. Using real-time quantitative PCR, the expression profiling of endochitinase gene was analyzed. Primary transformants and selfed progeny were examined for expression of the endochitinase using a fluorometric assay and for their resistance to the pathogenic fungi Botrytis cinerea and Rhizoctonia solani. The endochitinase activities in T0 in vitro plants, T0 mature plants and T1 mature plants were correlated with leaf lesions, and the transgenic line T618 had high endochitinse activities of 102.68, 114.53 and 120.27 nmol L–1 MU min–1 mg–1 protein in the three kinds of plants, respectively. The endochitinase activity showed a positive correlation with the resistance to the pathogens. Most transgenic T0 broccoli had increased resistance to the pathogens of B. cinerea and R. solani in leaf assays and this resistance was confirmed to be inheritable. These findings suggested that expression of the Tch gene from T. viride could enhance resistance to pathogenic fungi in Brassica species.

Reverse Genetic Approaches in Zebrafish

Zebrafish（Danio rerio） is a well-established vertebrate animal model.A comprehensive collection of reverse genetics tools has been developed for studying gene function in this useful organism.Morpholino is the most widely used reagent to knock down target gene expression post-transcriptionally.For a long time,targeted genome modification has been heavily relied on large-scale traditional forward genetic screens,such as ENU（N-ethyl-N-nitrosourea） mutagenesis derived TILLING（Targeting Induced Local Lesions IN Genomes） strategy and pseudo-typed retrovirus mediated insertional mutagenesis.Recently,engineered endonucleases,including ZFNs（zinc finger nucleases） and TALENs（transcription activator-like effector nucleases）,provide new and efficient strategies to directly generate site-specific indel mutations by inducing double strand breaks in target genes.Here we summarize the major reverse genetic approaches for loss-of-function studies used and emerging in zebrafish,including strategies based on genome-wide mutagenesis and methods for site-specific gene targeting.Future directions and expectations will also be discussed.

Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

Although quantitative trait loci（QTLs） for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes（SSCs） 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms（SNPs） associated with total number of thoracic-lumbar vertebrae and for each trait（number of thoracic and lumbar vertebrae） separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60 K chip. Performing a genome-wide association study（GWAS） for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor（NR6A1） on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin（VRTN）, prospero homeobox 2（PROX2）, Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog（FOS）, and transforming growth factor beta 3（TGFB3） may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.

Genome-Wide Analysis of Gene Expression in Stationary Phase and Genetic Characterization of Stationary-Phase-Dependent Halocin Gene Expression in the Haloarchaeon Haloferax mediterranei

The stationary phase of microbial growth is a very complex state regulated by various environmental and physiological factors. An intensive study of stationary phase could promote a comprehensive understanding of the complete life cycle of microorganisms, and may provide important insights into their adaptation to harsh and nutrient-depleted conditions. Although the underlying mechanisms have been weU-studied in bacteria and yeasts （Herman, 2002; Navarro Llorens et al., 2010）, less is known about this growth phase in archaea yet. The haloarchaeon Haloferax mediterranei has served as a good model for studying haloarchaeal physiology and metabolism for several decades because of its accelerated growth, remarkable metabolic ability and genomic stability （Han et al., 2012）. During stationary phase, H. mediterranei can produce halocin H4 （Cheung et al.,

Studying gene duplication and genetic variation of budding yeast:a systems and interdisciplinary approach

Budding yeast (Saccharomyces cerevisiae) is a single cell model organism that is amenable to genome wide experimental interrogation using high-throughput genomics, proteomics

Single nucleotide polymorphisms of the SCN5A gene in Han Chinese and their relation with Brugada syndrome

Background Mutations in the cardiac sodium channel gene (SCN5A) may lead to a broad spectrum of familial arrhythmias, including long QT syndrome (LQTS), idiopathic ventricular fibrillation (IVF), and isolated cardiac conduction diseases Recent studies have shown that polymorphisms in the SCN5A gene also play an important role in the manifestation of disorders involving cardiac excitability In this study, we investigated the polymorphisms of the SCN5A gene in Han Chinese and its relation to Brugada syndrome (BS) Methods Genomic DNA was isolated from 120 unrelated healthy volunteers and 48 unrelated Brugada syndrome patients by means of standard procedures All exons including the putative splicing sites of the SCN5A gene were amplified by PCR and sequenced directly or after subcloning using an ABI Prism 377 DNA sequencer Results A total of 5 single nucleotide polymorphisms (SNPs) were identified in the Han Chinese population, including 3 novel ones: G87A(A29A), 4245+82A>G, and G6174A The allele frequencies of each SNP in the Han Chinese population were as follows: G87A (A29A) 27 5%, A1673G (H558R) 10 4%, 4245+82A>G 32 8%, C5457T (D1819D) 41 3%, and G6174A 44 9% S1102Y and 10 other SNPs identified in other ethnic populations were not detected in this study There was no significant difference in the allele frequency of A1673G (H558R) between different ethnic populations (all P >0 5) On the other hand, the allele frequency of C5457T (D1819D) among Han Chinese was similar to its frequency among Japanese ( P >0 5), but higher than that among Americans ( P <0 005) The allele G1673 (R558) was over-represented in BS patients compared to controls ( P <0 005), but there was no significant difference in genotype frequencies at this locus There were also no differences in either the allele or genotype frequencies of the 4 other identified SNPs when comparing BS patients with healthy controls Conclusions The distribution of SCN5A SNPs may vary between different ethnicities The polymorphism of A1673G might be associated with BS and may contribute to a susceptibility to BS in Han Chinese

Retroviral endostatin gene transfer inhibits human colon cancer cell growth in vivo

Objective To investigate the therapeutic effect of retroviral endostatin gene transfer on the human colon cancer cell line,LoVo.Methods A retroviral vector pLESSN expressing secretable endostatin was constructed and packaged with a titer of 8.2×10 5 CFU/ml. A LoVo cell line was subjected to retrovirus-mediated endostatin gene transfer. The proviral integration of endostatin was analyzed with PCR. The function of endostatin was tested by MTT assay in vitro and a mouse xenograft model in vivo.Results After transfection and superinfection,amphotropic retrovirus was collected,and transduction with amphotropic retroviruses resulted in endostatin proviral integration. The endostatin secreted by transduced LoVo cells markedly inhibited endothelial cell growth up to 67% ( P <0.001),compared with the control cells. The gene expression of endostatin in LoVo colon tumor cells significantly inhibited tumor growth in vivo. There was an 86% reduction in tumor size in the endostatin-transduced group,accompanied by a reduction in vessels,compared with the control group ( P <0.01). Conclusion Retroviruses can allow functional expression of the endostatin gene in human colon tumors,showing promise for an antitumor strategy using antiangiogenesis.

Inhibitory effect of retroviral vector containing anti-sense Smad_4 gene on Ito cell line, LI90

Background Transforming growth factor-β1 (TGF-β1) exerts strong fibrogenic potential in culture-activated HSCs Smad 4 is a key intracellular mediator for the transforming growth factor-β (TGF-β) superfamily of growth factors The aim of this study was to assess the effects of the antisense Smad 4 gene on Ito cell line, LI90 Methods The recombinant retroviral vector pLXSN-Smad 4 was constructed by cloning the rat antisense Smad 4 cDNA into the retroviral vector pLXSN Retroviruses with or without the antisense gene were obtained by transfecting pLXSN-Smad 4 and pLXSN vectors into PA317 cells Human hepatic stellate cells (HSCs) LI90 were infected with these retroviruses followed by selection with G418 The expression of Smad 4 was detected by Northern and Western blots Cell biological characteristics, including cell growth curve, 3H-TdR and 3H-proline uptake by HSCs and the production of extracellular matrix were assessed Results mRNA and protein expressions of Smad 4 in LI90 cells transfected with retrovirus containing the antisense Smad 4 gene were much lower than those in LI90 cells transfected with empty vector or parental LI90 cells Cells hypoexpressing the Smad 4 gene exhibited a slower rate of growth, a lower uptake of 3H-TdR and 3H-proline ( P <0 01), and smaller production of th extracellular matrix, compared with parental LI90 cells and cells transfected with empty retrovirus Conclusions The antisense Smad 4 gene can suppress the expression of the Smad 4 gene, reduce endogenous production of Smad 4 mRNA and protein, block TGF-β1 signaling pathway, inhibit activation of Ito cells, obstruct the growth of Ito cells, decrease the production of the extracellular matrix (ECM) Our results may provide a basis for the development of antifibrotic gene therapy

High Accuracy Gene Signature for Chemosensitivity Prediction in Breast Cancer

Neoadjuvant chemotherapy for breast cancer patients with large tumor size is a necessary treatment.After this treatment patients who achieve a pathologic Complete Response（p CR） usually have a favorable prognosis than those without. Therefore, p CR is now considered as the best prognosticator for patients with neoadjuvant chemotherapy. However, not all patients can benefit from this treatment. As a result, we need to find a way to predict what kind of patients can induce p CR. Various gene signatures of chemosensitivity in breast cancer have been identified, from which such predictors can be built. Nevertheless, many of them have their prediction accuracy around 80%. As such, identifying gene signatures that could be employed to build high accuracy predictors is a prerequisite for their clinical tests and applications. Furthermore, to elucidate the importance of each individual gene in a signature is another pressing need before such signature could be tested in clinical settings. In this study, Genetic Algorithm（GA） and Sparse Logistic Regression（SLR） along with t-test were employed to identify one signature. It had 28 probe sets selected by GA from the top 65 probe sets that were highly overexpressed between p CR and Residual Disease（RD） and was used to build an SLR predictor of p CR（SLR-28）. This predictor tested on a training set（n = 81） and validation set（n = 52） had very precise predictions measured by accuracy,specificity, sensitivity, positive predictive value, and negative predictive value with their corresponding P value all zero. Furthermore, this predictor discovered 12 important genes in the 28 probe set signature. Our findings also demonstrated that the most discriminative genes measured by SLR as a group selected by GA were not necessarily those with the smallest P values by t-test as individual genes, highlighting the ability of GA to capture the interacting genes in p CR prediction as multivariate techniques. Our gene signature produced superior performance over a signature found in one previous study with prediction accuracy 92% vs 76%, demonstrating the potential of GA and SLR in identifying robust gene signatures in chemo response prediction in breast cancer.