Genetic basis of negative heterosis for growth traits in chickens revealed by genome-wide gene expression pattern analysis

Background:Heterosis is an important biological phenomenon that has been extensively utilized in agricultural breeding.However,negative heterosis is also pervasively observed in nature,which can cause unfavorable impacts on production performance.Compared with systematic studies of positive heterosis,the phenomenon of negative heterosis has been largely ignored in genetic studies and breeding programs,and the genetic mechanism of this phenomenon has not been thoroughly elucidated to date.Here,we used chickens,the most common agricultural animals worldwide,to determine the genetic and molecular mechanisms of negative heterosis.Results:We performed reciprocal crossing experiments with two distinct chicken lines and found that the body weight presented widely negative heterosis in the early growth of chickens.Negative heterosis of carcass traits was more common than positive heterosis,especially breast muscle mass,which was over−40%in reciprocal progenies.Genome-wide gene expression pattern analyses of breast muscle tissues revealed that nonadditivity,including dominance and overdominace,was the major gene inheritance pattern.Nonadditive genes,including a substantial number of genes encoding ATPase and NADH dehydrogenase,accounted for more than 68%of differentially expressed genes in reciprocal crosses(4257 of 5587 and 3617 of 5243,respectively).Moreover,nonadditive genes were significantly associated with the biological process of oxidative phosphorylation,which is the major metabolic pathway for energy release and animal growth and development.The detection of ATP content and ATPase activity for purebred and crossbred progenies further confirmed that chickens with lower muscle yield had lower ATP concentrations but higher hydrolysis activity,which supported the important role of oxidative phosphorylation in negative heterosis for growth traits in chickens.Conclusions:These findings revealed that nonadditive genes and their related oxidative phosphorylation were the major genetic and molecular factors in the negative heterosis of growth in chickens,which would be beneficial to future breeding strategies.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton. Results： In this study, we identified 22, 31, 55 and 60 SWEETgenes from the sequenced genomes of Gossypium orboreum, G. rairnondii, G. hirsutum and G. borbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification. Conclusion： SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEETgenes and more candidates for specific genetic modification, which will be useful in future research.

Analysis of Gene Expression Pattern of Lumbar Intervertebral Disc Degeneration in Human

ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.

Pattern of expression of the CREG gene and CREG protein in the mouse embryo

Background The cellular repressor of ElA-stimulated genes(CREG) is a secreted glycoprotein that inhibits cell proliferation and/or enhances differentiation.CREG is widely expressed in adult tissues such as the brain,heart, lungs,liver,intestines and kidneys in mice.We investigated the level of CREG expression during mouse embryogenesis and its distribution at 18.5 days post coitus(dpc).Methods Immunohistochemical staining with diaminobenzidine,western blotting and reverse transcription-polymerase chain reaction were used.Results CREG expression was rst detected in mouse embryos at 4.5 dpc.It was expressed at almost all stages up to 18.5 dpc.The level of CREG was found to increase gradually and was highest at 18.5 dpc.Western blotting showed that the CREG protein was expressed at higher levels in the brain,heart,intestines and kidneys than in the lungs and liver at 18.5 dpc.In 9.5 dpc embryos,CREG was expressed only in the endothelial cells of blood vessels,after the vascular lumen had formed.With advanced differentiation, vascular smooth muscle cells developed in the embryonic vascular structures;the expression of smooth muscle a-actin protein and CREG were positive and increased gradually in 10.5 dpc embryonic vessels.CREG expression in the embryonic blood vessels peaked at 15.5 dpc and was reduced slightly at 18.5 dpc.Conclusions These results indicate that CREG is expressed during mouse embryogenesis and might participate in the differentiation of these organs during embryogenesis.

Cloning, expression profiling and promoter functional analysis of bone morphogenetic protein 2 in the tongue sole(Cynoglossus semilaevis)

BMP2 plays crucial roles in vertebrate developmental process and acts as a bone inducer during osteogenesis. We present here the molecular cloning of bmp2 cDNA from the marine flatfish Cynoglossus semilaevis, and the analysis of bmp2 expression profiling and promoter function. The full length of bmp2 cDNA sequence is 2 048 bp,which encodes a protein of 422 amino acids. Tissue expression distribution of bmp2 was examined in 14 tissues of mature individuals by quantitative real time PCR（qRT-PCR）. The results revealed that bmp2 was expressed ubiquitously, and the highest expression level was detected in the spinal cord. Moreover, bmp2 expression levels were detected at 15 sampling time points of early developmental stages（egg, larva, juvenile and fingerling stages）.The highest expression level of bmp2 was observed at the gastrula stage, which was about ten times higher than those at the other three embryo stages. Whole-mount in situ hybridization showed that the bmp2 signal was strongly detected at the location of the crown-like larval fin, heart and liver, and slightly expressed in the notochord at one day post hatch（dph）; then the expression of bmp2 started to be concentrated in notochord at three dph. Subsequently, we characterized the 5′-flanking region of bmp2 by testing the promoter activity by Luciferase reporter assays. Positive regulatory region was detected at the location of –179 to ＋109. The predicted transcription factor binding sites（E-box binding factors, zinc finger transcription factor, etc.） in this region might participate in the transcriptional regulation of the bmp2 gene.

Developmental Temporal Patterns and Molecular Network Features in the Transcriptome of Rat Spinal Cord

The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals,especially in terms of their relationships with vital biological processes such as regeneration.Here,using a large-scale temporal transcriptomic analysis of rat spinal cord from the embryonic stage to adulthood,we show that fluctuating RNA expression levels reflect highly active transcriptional regulation,which may initiate spinal cord patterning.We also demonstrate that microRNAs(miRNAs)and transcriptional factors exhibit a mosaic profile based on their expression patterns,while differential alternative splicing events reveal that alternative splicing may be a driving force for the development of the node of Ranvier.Our study also supports the existence of a negative correlation between innate immunity and intrinsic growth capacity.Epigenetic modifications appear to perform their respective regulatory functions at different stages of development,while guanine nucleotidebinding protein(G protein)-coupled receptors(including olfactory receptors(ORs))may perform pleiotropic roles in axonal growth.This study provides a valuable resource for investigating spinal cord development and complements the increasing number of single-cell datasets.These findings also provide a genetic basis for the development of novel tissue engineering strategies.

Genome-Wide Analysis and Expression Patterns of the YUCCA Genes in Maize

Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;

Identifi cation and characterization of the bZIP transcription factor family in yellowhorn

The basic leucine zipper(bZIP)transcription factor family is one of the largest and most diverse families in plants,regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses.However,little is known about the biological functions of bZIP proteins in yellowhorn(Xanthoceras sorbifolium).Recently,64 XsbZIP genes were identifi ed in the yellowhorn genome and found to be disproportionately distributed in linkage groups.The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP,ZmbZIP and GmbZIP proteins.Five intron patterns in the basic and hinge regions and additional conserved motifs were defi ned,both supporting the group classifi cation and possibly contributing to their functional diversity.Compared to tandem duplication,the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes.In addition,most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions.Moreover,the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses,including salt(NaCl),cold and abscisic acid,with possibly diff erent molecular mechanisms.These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.

Time-series Analysis in Imatinib-resistant Chronic Myeloid Leukemia K562-cells under Different Drug Treatments

Chronic myeloid leukemia（CML） is characterized by the accumulation of active BCR-ABL protein. Imatinib is the first-line treatment of CML; however, many patients are resistant to this drug. In this study, we aimed to compare the differences in expression patterns and functions of time-series genes in imatinib-resistant CML cells under different drug treatments. GSE24946 was downloaded from the GEO database, which included 17 samples of K562-r cells with（n=12） or without drug administration（n=5）. Three drug treatment groups were considered for this study： arsenic trioxide（ATO）, AMN107, and ATO＋AMN107. Each group had one sample at each time point（3, 12, 24, and 48 h）. Time-series genes with a ratio of standard deviation/average（coefficient of variation） 〉0.15 were screened, and their expression patterns were revealed based on Short Time-series Expression Miner（STEM）. Then, the functional enrichment analysis of time-series genes in each group was performed using DAVID, and the genes enriched in the top ten functional categories were extracted to detect their expression patterns. Different time-series genes were identified in the three groups, and most of them were enriched in the ribosome and oxidative phosphorylation pathways. Time-series genes in the three treatment groups had different expression patterns and functions. Time-series genes in the ATO group（e.g. CCNA2 and DAB2） were significantly associated with cell adhesion, those in the AMN107 group were related to cellular carbohydrate metabolic process, while those in the ATO＋AMN107 group（e.g. AP2M1） were significantly related to cell proliferation and antigen processing. In imatinib-resistant CML cells, ATO could influence genes related to cell adhesion, AMN107 might affect genes involved in cellular carbohydrate metabolism, and the combination therapy might regulate genes involved in cell proliferation.

Identification of Rab family genes and functional analyses of LmRab5 and LmRab11A in the development and RNA interference of Locusta migratoria

Rab proteins constitute the largest family of small GTPases,which play pivotal roles in intracellular membrane trafficking in all eukaryotes.A number of Rab genes have been identified in eukaryotes;however,very little information about these genes has been reported in insects.In the current study,for the first time we identified and characterized 27 Rab family genes from Locusta migratoria.Phylogenetic analysis and comparison of domain architecture indicated that Rab family genes are highly conserved among insect species.Tissue-dependent expression profiles indicated that expression of Rab genes was highest in the ovary,except for LmRab3,which was most highly expressed in hemolymph.The biological function of each Rab gene was investigated using RNA interference(RNAi).Double-stranded RNA targeting each Rab gene was injected into the hemocoel of nymphs and revealed that suppression of two Rab genes(LmRab5 and LmRab11A)caused 100%mortality.In addition,nymphs injected with dsLmRab5 exhibited severe phenotypic defects in the gastric caeca and midgut,while dsLmRab11A arrested the molting process.We then applied the RNAi of RNAi technique to test if silencing either of these two genes would affect the suppression of the lethal giant larvae(LmLgl)reporter gene and found that suppression of LmRab5 diminished the RNAi efficiency of LmLgl,whereas suppression of LmRab11A enhanced RNAi efficiency of LmLgl.These results indicate that Rab genes contribute differently to RNAi efficiency in different tissues.Our study provides a foundation for further functional investigations of Rab genes and their contributions to RNAi efficiency in L.migratoria.