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1.
Genomics ; 112(1): 225-236, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30826444

RESUMO

Accurately predicting the phenotypes of complex traits is crucial to enhanced breeding in plants and livestock, and to enhanced medicine in humans. Here we reports the first study accurately predicting complex traits using their contributing genes, especially their number of favorable alleles (NFAs), genotypes and transcript expressions, with the grain yield of maize, Zea mays L. When the NFAs or genotypes of only 27 SNP/InDel-containing grain yield genes were used, a prediction accuracy of r = 0.52 or 0.49 was obtained. When the expressions of grain yield gene transcripts were used, a plateaued prediction accuracy of r = 0.84 was achieved. When the phenotypes predicted with two or three of the genic datasets were used for progeny selection, the selected lines were completely consistent with those selected by phenotypic selection. Therefore, the genes controlling complex traits enable accurately predicting their phenotypes, thus desirable for gene-based breeding in crop plants.

2.
Zhongguo Zhong Yao Za Zhi ; 44(21): 4634-4640, 2019 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-31872658

RESUMO

There is no consensus on the drying methods of Salvia miltiorrhiza in ancient and modern times,especially on the content of phenolic acid in fresh S. miltiorrhiza. In order to further explore the content of main components in fresh S. miltiorrhiza and study the dynamic changes during the drying process,the content of main components was used as the index in this study to evaluate the processing method,drying method,correlation between dehydration rate and component content for fresh S. miltiorrhiza. In addition,the sealed and unsealed parallel control groups were set to carry out verification test during the drying process. UPLC method was used for determination of seven main components including rosmarinic acid,lithosperic acid,salvianolic acid B,cryptotanshinone,tanshinoneⅠ,methylene salianolate and tanshinone ⅡAin S. miltiorrhiza. The results showed that the fresh S. miltiorrhiza contained low levels of phenolic acid,and the content of phenolic acid increased significantly with the increase of dehydration rate during drying process,while the change of tanshinone was not obvious. In the comparison of three drying methods,we found that drying at 50 ℃ was better than drying in the sun,and drying in the sun was superior to drying in the shade. So,drying at 50 ℃ was the best drying method. The correlation between dehydration and phenolic acid content of S. miltiorrhiza was analyzed by verification test and SPSS software,which further proved that the dehydration rate was significantly positively correlated with the content of phenolic acid components. This study provides reference for the production processing and drying methods of S. miltiorrhiza medicinal materials,which is of great significance for improving the quality of S. miltiorrhiza.


Assuntos
Salvia miltiorrhiza , Dessecação , Raízes de Plantas
3.
Theriogenology ; 140: 44-51, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31437668

RESUMO

Lysosome, an important organelle in eukaryotes, can sequester macromolecules submitted by the endocytosis and autophagy pathways for degradation and recycling. Massive macromolecular turnover is also vital to the growth and development of mammalian oocytes. However, the functional role of lysosomes in the meiotic maturation of mammalian oocytes remains largely unexplored. Here, by treating in vitro matured porcine cumulus-oocyte complexes (COCs) with chloroquine (CQ), a lysosome inhibitor, we showed that regardless of CQ concentration, lysosomal inhibition affected neither the extrusion of the first polar body (PB1), nor the ROS levels. However, CQ treatment dramatically decreased the rates of oocytes with normal chromosome alignment and cytoskeleton organization (P < 0.05), but boosted the rates of oocytes with apoptosis (P < 0.05). Subsequently, after pathenogenetic activation or in vitro fertilization, the death or fragmentation rates of oocytes treated by CQ (both 35 µM and 45 µM) were significantly higher (P < 0.05), whereas the rates of embryo cleavage, embryos developed to blastocysts, and average blastomere number per blastocyst, were all significantly lower (P < 0.05), respectively. Furthermore, CQ (35 µM) treatment activated the autophagy pathway by elevating the LC3 II/I ratio. Taken together, lysosomes could affect porcine oocyte maturation and subsequent developmental capacity partially through the chromosome organization/cytoskeleton assembly and autophagy/apoptosis pathways.

4.
Genomics ; 111(6): 1517-1528, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-30366041

RESUMO

Gene expression has been widely used in functional genomics research; however, the gene expressions quantified with different methods have been frequently inconsistent, thus challenging the conclusions from such research. Here we have addressed this issue, while taking into account RNA alternative splicing. We found that when a gene was subjected to RNA alternative splicing, it was impossible or difficult to properly quantify the expression of a transcript of the gene or its overall expression using quantitative real-time PCR (qPCR), Northern hybridization, microarray, or serial analysis of gene expression. Shot-gun RNA-seq was the most proper to quantify the expression of a transcript or a gene in such cases. Moreover, the expressions of individual transcripts quantified by shot-gun RNA-seq were highly reproducible (r = 0.90-0.98) between individuals. Therefore, shot-gun or full-length RNA-seq should be the method of choice to properly quantify the expression of a transcript or a gene.

5.
Theriogenology ; 121: 160-167, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30165304

RESUMO

Oocyte meiosis is a complex process coordinated by multiple endocrinal and molecular circuits. Recently, N6-methyladenosine (m6A) epigenetic modification on RNA is revealed to be important for meiotic maturation. However, the molecular mechanism of how m6A modification exerts its effect on oocyte maturation is largely unknown. Here, we showed that endogenous m6A writers (Mettl3 and Wtap) and eraser (Fto) elevated their transcript levels during meiotic maturation of pig oocytes. From germinal vesicle (GV) to metaphase II (MII) stages, global m6A level significantly increased, and existed mostly in ooplasm. Methyl donor (betaine, 16 mM) treatment of porcine cumulus-oocyte complexes (COCs) during in vitro maturation (IVM) significantly boosted nucleic acid m6A level within oocytes, but unchanged meiotic process and oocyte subsequent development. By contrast, methylation inhibitor (cycloleucine, 20 mM) reduced nucleic acid m6A level, and significantly decreased the germinal vesicle breakdown (GVBD) rate, the extrusion rate of the first polar body, and the cleavage and blastocyst rates of parthenotes. In addition, in cycloleucine-treated oocytes Wtap increased but Lin28 decreased their abundances significantly, along with the higher incidence of spindle defects and chromosome misalignment. Furthermore, pT161-CDK1 protein level in pig oocytes was confirmed to be decreased after cycloleucine treatment for 24 h. Taken together, chemical induced reduction of nucleic acid m6A methylation during pig oocyte meiosis could impair meiotic maturation and subsequent development potency, possibly through down-regulating pluripotency marker Lin28 mRNA abundance and disturbing MPF-regulated chromosome/spindle organization.


Assuntos
Metilação de DNA , Oócitos/citologia , Animais , Betaína/farmacologia , Proteína Quinase CDC2/genética , Proteína Quinase CDC2/metabolismo , Cicloleucina/farmacologia , Meiose/genética , Oócitos/efeitos dos fármacos , Oócitos/crescimento & desenvolvimento , Suínos/embriologia
6.
J Anim Sci ; 96(8): 3358-3369, 2018 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-29800308

RESUMO

Heat shock protein 90 (Hsp90) functions as a molecular chaperone in its interaction with clients to influence multiple cellular and physiological processes. However, our current understanding on Hsp90's relationship with mammalian oocyte maturation is still very limited. Here, we aimed to investigate Hsp90's effect on pig oocyte meiotic maturation. Endogenous Hsp90α was constantly expressed at both mRNA and protein levels in porcine maturing oocytes. Addition of 2 µM 17-allylamino-17-demethoxygeldanamycin (17-AAG), the Hsp90 inhibitor, to in vitro mature cumulus-oocyte complexes (COC) significantly decreased Hsp90α protein level (P < 0.05), delayed germinal vesicle breakdown (GVBD) (P < 0.05), and impeded the first polar body (PB1) extrusion (P < 0.01) of porcine oocytes. 2 µM 17-AAG treatment during in vitro maturation also decreased the subsequent development competence as indicated by the lower cleavage (P < 0.001) and higher fragmentation (P < 0.001) rates of parthenotes, whereas no effects on the percentage and average cell number of blastocysts were found. Immunodepletion of Hsp90α by antibody microinjection into porcine oocytes at germinal vesicle and metaphase II stages induced similar defects of meiotic maturation and parthenote development, to that resulted from 2 µM inhibitor 17-AAG. For oocytes treated by 2 µM 17-AAG, the cytoplasm and membrane actin levels were weakened (P < 0.01), and the spindle assembly was disturbed (P < 0.05), due to decreased p-ERK1/2 level (P < 0.05). However, the mitochondrial function and early apoptosis were not affected, as demonstrated by rhodamine 123 staining and Annexin V assays. Our findings indicate that Hsp90α can couple with mitogen-activated protein kinase to regulate cytoskeletal structure and orchestrate meiotic maturation of porcine oocytes.


Assuntos
Proteínas de Choque Térmico/metabolismo , Técnicas de Maturação in Vitro de Oócitos/veterinária , Sistema de Sinalização das MAP Quinases , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Suínos/fisiologia , Animais , Feminino , Oócitos/fisiologia
7.
Sci Rep ; 8(1): 6132, 2018 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-29666467

RESUMO

L-ascorbic acid (Vitamin C) can enhance the meiotic maturation and developmental competence of porcine oocytes, but the underlying molecular mechanism remains obscure. Here we show the role of ascorbic acid in regulating epigenetic status of both nucleic acids and chromatin to promote oocyte maturation and development in pigs. Supplementation of 250 µM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P) during in vitro maturation significantly enhanced the nuclear maturation (as indicated by higher rate of first polar body extrusion and increased Bmp15 mRNA level), reduced level of reactive oxygen species, and promoted developmental potency (higher cleavage and blastocyst rates of parthenotes, and decreased Bax and Caspase3 mRNA levels in blastocysts) of pig oocytes. AA2P treatment caused methylation erasure in mature oocytes on nucleic acids (5-methylcytosine (5 mC) and N 6 -methyladenosine (m6A)) and histones (Histone H3 trimethylations at lysines 27, H3K27me3), but establishment of histone H3 trimethylations at lysines 4 (H3K4me3) and 36 (H3K36me3). During the global methylation reprogramming process, levels of TET2 (mRNA and protein) and Dnmt3b (mRNA) were significantly elevated, but simultaneously DNMT3A (mRNA and protein), and also Hif-1α, Hif-2α, Tet3, Mettl14, Kdm5b and Eed (mRNA) were significantly inhibited. Our findings support that ascorbic acid can reprogram the methylation status of not only DNA and histone, but also RNA, to improve pig oocyte maturation and developmental competence.


Assuntos
Antioxidantes/farmacologia , Ácido Ascórbico/farmacologia , Epigênese Genética/efeitos dos fármacos , Oócitos/efeitos dos fármacos , Oogênese/efeitos dos fármacos , Suínos/crescimento & desenvolvimento , Animais , Proteína Morfogenética Óssea 15/genética , Células Cultivadas , Metilação de DNA/efeitos dos fármacos , Feminino , Oócitos/citologia , Oócitos/metabolismo , RNA Mensageiro/genética , Espécies Reativas de Oxigênio/metabolismo , Suínos/genética , Suínos/metabolismo
8.
J Biol Chem ; 293(5): 1767-1780, 2018 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-29222335

RESUMO

The brilliant cresyl blue (BCB) test is used in both basic biological research and assisted reproduction to identify oocytes likely to be developmentally competent. However, the underlying molecular mechanism targeted by the BCB test is still unclear. To explore this question, we first confirmed that BCB-positive porcine oocytes had higher rates of meiotic maturation, better rates of cleavage and development into blastocysts, and lower death rates. Subsequent single-cell transcriptome sequencing on porcine germinal vesicle (GV)-stage oocytes identified 155 genes that were significantly differentially expressed between BCB-negative and BCB-positive oocytes. These included genes such as cdc5l, ldha, spata22, rgs2, paip1, wee1b, and hsp27, which are enriched in functionally important signaling pathways including cell cycle regulation, oocyte meiosis, spliceosome formation, and nucleotide excision repair. In BCB-positive GV oocytes that additionally had a lower frequency of DNA double-strand breaks, the CDC5L protein was significantly more abundant. cdc5l/CDC5L inhibition by short interference (si)RNA or antibody microinjection significantly impaired porcine oocyte meiotic maturation and subsequent parthenote development. Taken together, our single-oocyte sequencing data point to a potential new role for CDC5L in porcine oocyte meiosis and early embryo development, and supports further analysis of this protein in the context of the BCB test.


Assuntos
Proteínas de Ciclo Celular , Sequenciamento de Nucleotídeos em Larga Escala , Meiose/fisiologia , Oócitos/metabolismo , Transcriptoma/fisiologia , Animais , Proteínas de Ciclo Celular/biossíntese , Proteínas de Ciclo Celular/genética , Feminino , Oócitos/citologia , Suínos
9.
Yi Chuan ; 39(9): 837-846, 2017 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-28936981

RESUMO

Endogenous circadian rhythms play a key role in regulating plant growth and development, and in allowing plants to respond and adapt to changing environments. To understand how drought regulates upland rice(Oryza sativa L.) IRAT109, we examined the expression levels of circadian clock and drought-responsive genes through real-time PCR. The results revealed that, first, drought reduced the relative expression level and amplitude of peak expression of several morning circadian clock components (such as OsPRRs, OsLHY and OsZTL1), increased the relative expression level and amplitude of some evening circadian clock components (such as OsTOC1, OsGI and OsELF3), but did not influence OsFKF1. Secondly, the relative expression level of most drought-responsive genes was generally increased, except for OsDST, a negative regulator. Lastly, expression rhythms of most drought-responsive genes were disturbed, but not that of OsCIPK12, OsCDPK7 and OsDREB1A. The results indicate that drought stress modulates the expression of circadian clock components and the interplay regulates diurnal oscillations of relative genes.


Assuntos
Relógios Circadianos/genética , Ritmo Circadiano/genética , Regulação da Expressão Gênica de Plantas/genética , Oryza/genética , Estresse Fisiológico/genética , Secas , Genes de Plantas/genética , Proteínas de Plantas/genética
10.
Zhong Yao Cai ; 38(6): 1212-6, 2015 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-26762063

RESUMO

OBJECTIVE: To identify Chuanxiong Rhizoma,Angelicae Sinensis Radix and Ligustici Rhizoma et Radix by establishing the HPLC specific chromatograms of their volatile oil and to compare their specific peaks. METHODS: The HPLC method used methanol-water as mobile phase. Their specific peaks were analysed by HPLC-MS. RESULTS: Under the selected spectrum condition, their HPLC specific chromatograms were established. Senkyunolide A, butylphalide, coniferylferulate, E-ligustilide, Z-ligustilide, neocnidilide and E-butylidenephthalide were identified as specific peaks in chromatograms based on their MS data. CONCLUSION: This method is simple, accurate and available to identify Chuanxiong Rhizoma, Angelicae Sinensis Radix and Ligustici Rhizoma et Radix. It provides reference for quality control of their medicinal materials and Chinese Patent Medicine.


Assuntos
Angelica sinensis/química , Medicamentos de Ervas Chinesas/química , Ligusticum/química , Óleos Voláteis/química , Óleos Vegetais/química , 4-Butirolactona/análogos & derivados , Benzofuranos , Cromatografia Líquida de Alta Pressão , Anidridos Ftálicos , Raízes de Plantas/química , Rizoma/química
11.
Genome ; 57(1): 9-19, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24564211

RESUMO

Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear "jigsaw puzzle". Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice.


Assuntos
Arabidopsis/genética , DNA Fúngico/química , DNA de Plantas/química , Oryza/genética , Saccharomyces cerevisiae/genética , Expansão das Repetições de DNA , Evolução Molecular , Genoma Fúngico , Genoma de Planta , Repetições de Microssatélites , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Retroelementos , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
13.
J Agric Food Chem ; 58(19): 10545-52, 2010 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-20839801

RESUMO

The present study was performed to understand the effects of high temperature (HT) during filling on the expression of storage proteins and the quality of rice grains. HT (35/30 °C day/night) reduced the weight, amylose content, and flour gel consistency of grains. It increased the accumulation of all classes of storage proteins at early filling stage but decreased the accumulation of prolamins at maturation. For albumins, the expressions of cyclophilin 2, peroxiredoxin, and HSP16.9 were differentially enhanced by HT. For globulins, HT decreased the accumulation of globulin but increased that of glyoxalase I and peroxiredoxin. HT enhanced the transcription of genes for glutelins, prolamins, globulins, and protein disulfide isomerase at early filling stage but decreased the expression of these genes at a later stage. Low amounts of prolamins and globulins, as well as low pH value, were found in sound, immature, and dead kernels grown under HT. The relationships among HT, storage proteins, and grain quality are discussed.


Assuntos
Temperatura Alta , Oryza/química , Proteínas de Armazenamento de Sementes/análise , Concentração de Íons de Hidrogênio , Controle de Qualidade , RNA Mensageiro/análise , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Proteínas de Armazenamento de Sementes/genética , Sementes/química , Espectrometria de Massas em Tandem
14.
Nucleic Acids Res ; 38(19): 6513-25, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-20542917

RESUMO

Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their 'surplus' genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms' phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism's morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.


Assuntos
Genes de Plantas , Variação Genética , Família Multigênica , Evolução Molecular , Fabaceae/genética , Genoma de Planta , Gossypium/genética , Oryza/genética , Filogenia , Plantas/classificação , Plantas/genética , Poliploidia , Seleção Genética
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