Copy-number variation in goat genome sequence: A comparative analysis of the different litter size trait groups.

Copy number variation (CNV), as an important component of genomic structural variation (SV), plays essential roles in phenotypic variability, disease susceptibility and species evolution. To investigate whether critical CNVs exist in dairy goats with differing fecundity, we performed genome-wide sequencing of two populations of Laoshan dairy goats with large differences in litter size. After reference genome aligning, CNV calling, and annotation, we screened identified CNVs in the high-fecundity (HF) and low-fecundity (LF) groups to identify discrepant CNVs and their distribution within the genome. Prolactin-related protein 1 and 6 (PRP1 and PRP6), important factors regulating reproductive processes, were demonstrated to be duplicated in the HF group. In summary, based on the differences in CNVs between goats with differing litter sizes, it suggests CNVs may contribute to litter size in Laoshan dairy goats.

Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing.

Genome flanking regions surrounding transcription start sites (TSSs) are critical for the regulation of gene expression, containing many translational regulatory elements. To investigate whether critical single nucleotide polymorphisms (SNPs) exist around TSSs in the dairy goat genome, we performed high throughput DNA sequencing to compare two dairy goat groups with discrepant litter sizes. After genome mapping, SNP calling, and annotation, we screened the SNPs within 2kb scales surrounding annotated TSSs in high fecundity (HF) and low fecundity (LF) groups, respectively. We attempted to identify distinct SNPs and motifs near the TSSs in both groups. The SNPs near the TSSs most were consistent; 318 new SNPs were uncovered in the HF group, of which 305 were heterozygote SNPs, 13 were homozygote SNPs, and majority of which were distributed on chromosome 2 and 29. After validation by Sanger sequencing we found that a SNP in CHI16: 27612330 C>A in the PSEN2 gene presented an A/A genotype in the HF group and an A/A or A/C genotype in the LF group. In conclusion, our study provides insightful information into the dairy goat genomic variations surrounding TSSs, which may contribute to enhanced litter size. Based on comparison studies of SNPs exist around transcription start sites between high fecundity group and low fecundity group. Our finding provides insights concerning the goat litter size phenotypic and will promote future goat breeding.

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus).

Dairy goats are one of the most utilized domesticated animals in China. Here, we selected extreme populations based on differential fecundity in two Laoshan dairy goat populations. Utilizing deep sequencing we have generated 68.7 and 57.8 giga base of sequencing data, and identified 12,458,711 and 12,423,128 SNPs in the low fecundity and high fecundity groups, respectively. Following selective sweep analyses, a number of loci and candidate genes in the two populations were scanned independently. The reproduction related genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 and THEM4 were specifically selected in the high fecundity group whereas KDM6A, TENM1, SWI5 and CYM were specifically selected in the low fecundity group. A sub-set of genes including SYCP2, SOX5 and POU3F4 were localized both in the high and low fecundity selection windows, suggesting that these particular genes experienced strong selection with lower genetic diversity. From the genome data, the rare nonsense mutations may not contribute to fecundity, whereas nonsynonymous SNPs likely play a predominant role. The nonsynonymous exonic SNPs in SETDB2 and CDH26 which were co-localized in the selected region may take part in fecundity traits. These observations bring us a new insights into the genetic variation influencing fecundity traits within dairy goats.

Association of ß2-microglobulin with the prognosis of non-Hodgkin's lymphoma: a meta analysis.

OBJECTIVE: The influence of ß2-microglobulin (ß2-MG) on the prognosis of non-Hodgkin's lymphoma (NHL) remains controversial. This study performed meta-analyses to evaluate the prognostic value of ß2-MG on the overall survival (OS) of NHL. METHODS: Through a search of relevant literature in PubMed, EMbase, Science Direct, OVID and Wanfang databases from 1980-2013, the hazard ratios (HRs) of OS between the normal ß2-MG group and the increased ß2-MG group were retrieved, and the results were combined using a fixed effect model and a random effect model. Subgroup analyses were performed based on univariate and multivariate analysis results, and sensitivity analyses were performed to estimate the changes of the combined HRs. In addition, funnel plots and fail-safe numbers were used to estimate publication bias. RESULTS: A total of 17 qualified publications were included, with a cumulative total of 2,479 cases. The result of heterogeneity examination showed that there was heterogeneity among all studies (P < 0.001, I(2) = 87%). In the random effect model, the combined HR was 2.71 (95% confidence interval [CI]: 1.91-3.85). The result of the total effect examination was statistically significant (Z = 5.59, P < 0.001). CONCLUSION: The increased ß2-MG level was an independent risk factor for the prognosis of NHL.

Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice.

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F(1) super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F(1) hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F(1) hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage.

Cell-wall invertase plays an important role in sucrose partitioning between source and sink organs in higher plants. To investigate the role of cell-wall invertases for seed development in rice (Oryza sativa L.), cDNAs of three putative cell-wall invertase genes OsCIN1, OsCIN2 and OsCIN3 were isolated. Semi-quantitative reverse transcription-polymerase chain reaction analysis revealed different expression patterns of the three genes in various rice tissues/organs. In developing caryopses, they exhibited similar temporal expression patterns, expressed highly at the early and middle grain filling stages and gradually declined to low levels afterward. However, the spatial expression patterns of them were very different, with OsCIN1 primarily expressed in the caryopsis coat, OsCIN2 in embryo and endosperm, and OsCIN3 in embryo. Further RNA in situ hybridization analysis revealed that a strong signal of OsCIN2 mRNA was detected in the vascular parenchyma surrounding the xylem of the chalazal vein and the aleurone layer, whereas OsCIN3 transcript was strongly detected in the vascular parenchyma surrounding the phloem of the chalazal vein, cross-cells, the aleurone layer and the nucellar tissue. These data indicate that the three cell-wall invertase genes play complementary/synergetic roles in assimilate unloading during the grain filling stage. In addition, the cell type-specific expression patterns of OsCIN3 in source leaf blades and anthers were also investigated, and its corresponding physiological roles were discussed.

Cloning and expression analysis of rice sucrose transporter genes OsSUT2M and OsSUT5Z.

Two sucrose transporter (SUT) cDNAs, OsSUT2M and OsSUT5Z, were isolated from rice (Oryza sativa L.) by reverse transcription polymerase chain reaction (RT-PCR). Sequencing results indicate they are 1,531 bp and 1,635 bp in length including complete open reading frame 1,506 bp and 1,608 bp, which encode 502 amino acids and 536 amino acids, respectively. The TopPred program suggested that both sucrose transporter proteins, OsSUT2M and OsSUT5Z, consist of potentially 12 transmembrane domains. Semi-quantitative RT-PCR was carried out to investigate the gene expression patterns of OsSUT2M and OsSUT5Z. In vegetative organs, transcripts of OsSUT2M were higher in source leaf blades than in other organs at the same development stage, whereas transcripts of OsSUT5Z were less traceable in all organs investigated. In reproductive organs, both transcripts of these two genes were high in panicles from the booting stage to 7 days after flowering (DAF) and then sharply declined. The potential physiology functions of these two sucrose transporters are discussed.