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Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers. We applied ridge regression best linear unbiased prediction coupled with fivefold cross-validations and evaluated three strategies of marker preselection. For plant height, marker density and marker preselection procedure impacted prediction accuracy only marginally. In contrast, for grain yield, prediction accuracy based on markers selected with a haplotype block analyses-based approach increased by approximately 4 % compared with random or equidistant marker sampling. Thus, applying marker preselection based on haplotype blocks is an interesting option for a cost-efficient implementation of genomic selection for grain yield in soybean breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0504-9) contains supplementary material, which is available to authorized users.

Summary Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. After an anoxic pre‐incubation, denitrification rates moderately increased and the N2O/(N2O + N2) ratios declined while the microbial abundance and diversity did not change significantly in most of the layers. Denitrification rate was significantly enhanced and the abundance of the denitrification genes was simultaneously elevated by the increased availability of organic carbon in all studied layers, to a greater extent in the subsurface layers than in the surface layers, suggesting the severe scarcity of carbon in the deep vadose zone. The genera Pseudomonas and Bacillus, which are made up of a number of species that have been previously identified as denitrifiers in soil, were the major taxa that respond to carbon addition. Overall, our results suggested that the limited denitrification in the deep vadose zone is not because of the lack of denitrifiers, but due to the low abundance of denitrifiers which is caused by low carbon availability.

BackgroundWe previously showed that the fatty liver formations observed in overfed geese are accompanied by the activation of the PI3K-Akt-mTOR pathway and an increase in plasma insulin concentrations. Recent studies have suggested a crucial role for the PI3K-Akt-mTOR pathway in regulating lipid metabolism; therefore, we hypothesized that insulin affects goose hepatocellular lipid metabolism through the PI3K-Akt-mTOR signaling pathway.MethodsGoose primary hepatocytes were isolated and treated with serum-free media supplemented with PI3K-Akt-mTOR pathway inhibitors (LY294002, rapamycin, and NVP-BEZ235, respectively) and 50 or 150 nmol/L insulin.ResultsInsulin induced strong effects on lipid accumulation as well as the mRNA and protein levels of genes involved in lipogenesis, fatty acid oxidation, and VLDL-TG assembly and secretion in primary goose hepatocytes. The stimulatory effect of insulin on lipogenesis was significantly decreased by treatment with PI3K-Akt-mTOR inhibitors. These inhibitors also rescued the insulin-induced down-regulation of fatty acid oxidation and VLDL-TG assembly and secretion.ConclusionThese findings suggest that the stimulatory effect of insulin on lipid deposition is mediated by PI3K-Akt-mTOR regulation of lipogenesis, fatty acid oxidation, and VLDL-TG assembly and secretion in goose hepatocytes.

Phosphatidylinositol-3 kinases (PI3K)-Protein kinase B (Akt)-mammalian target of rapamycin (mTOR) pathway plays an important role in the synthesis and secretion of triacylglycerol. However, the mechanism of PI3K-Akt-mTOR pathway in regulating lipid metabolism of goose liver was poorly understood. The purpose of this study was to determine how PI3K-Akt-mTOR pathway regulating lipid metabolic homeostasis in goose hepatocytes. Goose primary hepatocytes were treated with different PI3K-Akt-mTOR signal inhibitors (LY294002, rapamycin and NVP-BEZ235) for 24 h. The results showed that these inhibitors evidently inhibited PI3K-Akt-mTOR downstream signaling. Meanwhile, these PI3K-Akt-mTOR inhibitors reduced intracellular lipid accumulation, decreased the mRNA expression and protein content of genes involved in the de novo fatty acid synthesis, while increased the transcriptional and protein level of key factors involved in fatty acid oxidation and very low density lipoprotein (VLDL) assembly and secretion. Conclusion: These findings suggested that the reduction of lipids accumulation induced-by inhibiting PI3K-Akt-mTOR pathway was closely linked to the decrease of lipogenesis, the increase of fatty acids oxidation, and the increase of VLDL assembly and secretion in goose hepatocytes.

BackgroundThe pistillody mutant wheat (Triticum aestivum L.) plant HTS-1 exhibits homeotic transformation of stamens into pistils or pistil-like structures. Unlike common wheat varieties, HTS-1 produces three to six pistils per floret, potentially increasing the yield. Thus, HTS-1 is highly valuable in the study of floral development in wheat. In this study, we conducted RNA sequencing of the transcriptomes of the pistillody stamen (PS) and the pistil (P) from HTS-1 plants, and the stamen (S) from the non-pistillody control variety Chinese Spring TP to gain insights into pistil and stamen development in wheat.ResultsApproximately 40 Gb of processed reads were obtained from PS, P, and S. De novo assembly yielded 121,210 putative unigenes, with a mean length of 695 bp. Among these high-quality unigenes, 59,199 (48.84%) had at least one significant match with an existing gene model. A total of 23, 263, and 553 differentially expressed genes were identified in PS vs. P, PS vs. S, and P vs. S, respectively, with differences in expression greater than five-fold. Among the differentially expressed genes, 206 were highly correlated with stamen and pistil development. These genes include WM27B, DL, YAB1, YABBY4, WM 5, CER 1, and WBLH1, which have been implicated in flower development. The expression patterns of 25 differentially expressed genes were confirmed through quantitative real-time reverse transcription PCR.ConclusionsAnalysis of this transcriptome resource enabled us to characterize gene expression profiles, examine differential gene expression, and produce a candidate gene list related to wheat stamen and pistil development. This work is significant for the development of genomic resources for wheat, and provides important insights into the molecular mechanisms of wheat stamen and pistil development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1453-0) contains supplementary material, which is available to authorized users.

BackgroundThe wheat mutant line three-pistil (TP) exhibits three pistils per floret. As TP normally has two or three seeds in each of the florets on the same spike, there is the possibility of increasing the number of grains per spike. Therefore, TP is a highly valuable mutant for breeding and for the study of floral development in wheat. To map the three-pistil gene (Pis1), genotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) data from an F2 mapping population (CM28 × CM28TP) was used to construct a genetic map that is of significant value.ResultsIn the present study, a high-density genetic map of wheat containing 2917 GBS-SNP markers was constructed. Twenty-one linkage groups were resolved, with a total length of 2371.40 cM. The individual chromosomes range from 2.64 cM to 454.55 cM with an average marker density of 0.81 cM. The Pis1 gene was mapped using this high-resolution map, and two flanking SNP markers tightly linked to the gene, M70 and M71, were identified. The Pis1 is 3.00 cM from M70 and 1.10 cM from M71. In bread wheat genome, M70 and M71 were found to delimit a physical distance of 3.40 Mb, which encompasses 127 protein-coding genes. To validate the GBS-generated genotypic data and to eliminate missing marker data in the Pis1 region, five Kompetitive Allele-Specific PCR (KASP) assays were designed from corresponding GBS sequences, which harbor SNPs that surround Pis1. Three KASP-SNP markers, KM70, KM71, and KM75, were remapped to the Pis1 gene region.ConclusionsThis work not only lays the foundation for the map-based cloning of Pis1 but can also serve as a valuable tool for studying marker-trait association of important traits and marker-assisted breeding in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3960-7) contains supplementary material, which is available to authorized users.

Background/Aims: Recent studies have suggested a crucial role for PI3K-Akt-mTOR pathway in regulating cell proliferation, so we hypothesize that insulin acts goose hepatocellular growth by PI3K-Akt-mTOR signal pathway. Because the physiological status of liver cells in vitro is different from that in vivo, a simplified cell model in vitro was established. Methods: Goose primary hepatocytes were isolated and incubated in either no addition as a control or insulin or PI3K-Akt-mTOR pathway inhibitors or co-treatment with glucose and PI3K-Akt-mTOR pathway inhibitors; Then, cell DNA synthesis and cell cycle analysis were detected by BrdU-incorporation Assay and Flow cytometric analysis; the mRNA expression and protein expression of factors involved in the cell cycle were determined by Real-Time RT-PCR, ELISA, and western blot. Results: Here we first showed that insulin evidently increased the cell DNA synthesis, the mRNA level and protein content of factors involved in the cell proliferation of goose primary hepatocytes. Meanwhile, insulin evidently increased the mRNA level and protein content of factors involved in PI3K-Akt-mTOR pathway. However, the up-regulation of insulin on cell proliferation was decreased significantly by the inhibitors of PBK-Akt-mTOR pathway, LY294002, rapamycin or NVP-BEZ235. Conclusion: These findings suggest that PI3K-Akt-mTOR pathway plays an essential role in insulin-regulated cell proliferation of goose hepatocyte.