Predicting the accuracy of genomic predictions.

BACKGROUND: Mathematical models are needed for the design of breeding programs using genomic prediction. While deterministic models for selection on pedigree-based estimates of breeding values (PEBV) are available, these have not been fully developed for genomic selection, with a key missing component being the accuracy of genomic EBV (GEBV) of selection candidates. Here, a deterministic method was developed to predict this accuracy within a closed breeding population based on the accuracy of GEBV and PEBV in the reference population and the distance of selection candidates from their closest ancestors in the reference population. METHODS: The accuracy of GEBV was modeled as a combination of the accuracy of PEBV and of EBV based on genomic relationships deviated from pedigree (DEBV). Loss of the accuracy of DEBV from the reference to the target population was modeled based on the effective number of independent chromosome segments in the reference population (Me). Measures of Me derived from the inverse of the variance of relationships and from the accuracies of GEBV and PEBV in the reference population, derived using either a Fisher information or a selection index approach, were compared by simulation. RESULTS: Using simulation, both the Fisher and the selection index approach correctly predicted accuracy in the target population over time, both with and without selection. The index approach, however, resulted in estimates of Me that were less affected by heritability, reference size, and selection, and which are, therefore, more appropriate as a population parameter. The variance of relationships underpredicted Me and was greatly affected by selection. A leave-one-out cross-validation approach was proposed to estimate required accuracies of EBV in the reference population. Aspects of the methods were validated using real data. CONCLUSIONS: A deterministic method was developed to predict the accuracy of GEBV in selection candidates in a closed breeding population. The population parameter Me that is required for these predictions can be derived from an available reference data set, and applied to other reference data sets and traits for that population. This method can be used to evaluate the benefit of genomic prediction and to optimize genomic selection breeding programs.

Enhanced Potentiometric Hydrogen Sensing Response Based on the Ba0.5Sr0.5Co1-yFeyO3-δ Electrode with Unusual Polarity.

In this work, unusual potentiometric hydrogen sensing of mixed conducting Ba0.5Sr0.5Co0.8Fe0.2O3-δ was reported. Inspired by the unusual polarity, a dual sensing electrode (SE) potentiometric hydrogen sensor was fabricated by pairing Ba0.5Sr0.5Co0.8Fe0.2O3-δ with electronic conducting ZnO to enhance the hydrogen response. Hydrogen sensing measurements suggested that significantly higher response, larger sensitivity, and lower limit of detection (LOD) were achieved by the dual SE sensor when compared with the single SE sensor based on Ba0.5Sr0.5Co0.8Fe0.2O3-δ or ZnO. A high response of 97.3 mV for 500 ppm hydrogen and a low LOD of 2.5 ppm were obtained by the dual SE sensor at 450 °C. Furthermore, the effect of the Fe doping concentration in Ba0.5Sr0.5Co1-yFeyO3-δ (y = 0.2, 0.5, and 0.8) on hydrogen sensing response was investigated. The potentiometric response values to hydrogen increased monotonically with increasing Fe doping concentration. With the Fe/Co atomic ratio increased from 0.25 to 4, the responses to 500 ppm hydrogen raised by 69.6 and 94% at 350 and 450 °C, respectively. The sensing behaviors of unusual Ba0.5Sr0.5Co1-yFeyO3-δ may be ascribed to the predominant surface electrostatic effect. These results show that mixed conducting Ba0.5Sr0.5Co1-yFeyO3-δ is desirable for developing high-performance dual SE hydrogen sensors.

One-dimensional MOF-derived magnetic composites for efficient microwave absorption at ultralow thickness through controllable hydrogen reduction.

Magnetic materials with ingeniously designed structures may be utilized as highly efficient microwave absorbing materials (MAMs) working at ultralow matching thicknesses. However, it remains a challenge to decrease the matching thickness by synergistically tailoring the composition and structure of magnetic MAMs. In this work, a series of magnetic MAMs have been synthesized by sequentially annealing Fe-bdc nanorods in air and hydrogen. The results show that with the increase in hydrogen reduction temperature, the Fe2O3 nanorods would be gradually converted into Fe2O3/Fe3O4/C, Fe3O4/C, Fe3O4/FeO/Fe/C and Fe/C composites. In the meantime, obvious particle shrinkage would first occur and significant crystal growth would then happen, leading to the disappearance of pores, the decrease in axial length and the increase in particle size. In addition, a higher reduction temperature always leads to higher complex permittivity (εr) and permeability (µr), which should be related to the higher content of Fe3O4 and Fe. Nevertheless, one-dimensional structures and surface oxidation may cause abnormal εr and µr. As for HR-350, the one-dimensional structure results in strong conduction loss, the Fe3O4/C interfaces contribute to polarization loss, and semiconductive Fe3O4 and amorphous carbon favor superior impedance matching. Consequently, an RL peak value of -43.77 dB can be obtained with an effective absorption bandwidth of 3.52 GHz, when the thickness is only 1.2 mm. This work may provide novel insights into the design of MAMs with broadband absorption at ultralow matching thicknesses and provide a good reference for the synthesis of MOF-derived magnetic materials.

Melamine-induced formation of carbon nanotubes assembly on metal-organic framework-derived Co/C composites for lightweight and broadband microwave absorption.

Extending effective absorption bandwidth at a low filling ratio is still a challenge for metal-organic framework-derived microwave absorbing materials. Herein, varied complex structures based on CNTs have been built on Co/C particles derived from ZIF-67 via melamine-involved annealing routes. It was found that cobalt nanoparticles derived from ZIF-67 act as catalysts for the growth of CNTs, effectively promoting and controlling the content of melamine. Due to the effective control of the CNT-containing complex structure, excellent microwave absorption performance was achieved at a rather low filling ratio of 20 wt%, which can be attributed to improved attenuation ability and ameliorated impedance matching. Results show that highly graphitic CNTs benefit the formation of the electron transport network and enhancement of conduction loss. Unique one-dimensional complex structure and abundant Co/C interfaces strengthen the polarization loss. When the dielectric loss was optimized at different frequencies, appropriate impedance matching was also gained to realize a broad effective absorption bandwidth of 5.6 and 4.4 GHz in Ku and X bands, respectively. This work may provide novel insights into the synthesis and design of CNT-containing metal-organic framework-derived materials with lightweight features and wide frequency response.

Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens.

BACKGROUND: The frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features. The objective of this study was to assess the frequency of recombination events and to identify QTL (quantitative trait loci) for recombination rate in two purebred layer chicken lines. METHODS: A total of 1200 white-egg layers (WL) were genotyped with 580 K SNPs and 5108 brown-egg layers (BL) were genotyped with 42 K SNPs (single nucleotide polymorphisms). Recombination events were identified within half-sib families and both the number of recombination events and the recombination rate was calculated within each 0.5 Mb window of the genome. The 10% of windows with the highest recombination rate on each chromosome were considered to be recombination hotspots. A BayesB model was used separately for each line to identify genomic regions associated with the genome-wide number of recombination event per meiosis. Regions that explained more than 0.8% of genetic variance of recombination rate were considered to harbor QTL. RESULTS: Heritability of recombination rate was estimated at 0.17 in WL and 0.16 in BL. On average, 11.3 and 23.2 recombination events were detected per individual across the genome in 1301 and 9292 meioses in the WL and BL, respectively. The estimated recombination rates differed significantly between the lines, which could be due to differences in inbreeding levels, and haplotype structures. Dams had about 5% to 20% higher recombination rates per meiosis than sires in both lines. Recombination rate per 0.5 Mb window had a strong negative correlation with chromosome size and a strong positive correlation with GC content and with CpG island density across the genome in both lines. Different QTL for recombination rate were identified in the two lines. There were 190 and 199 non-overlapping recombination hotspots detected in WL and BL respectively, 28 of which were common to both lines. CONCLUSIONS: Differences in the recombination rates, hotspot locations, and QTL regions associated with genome-wide recombination were observed between lines, indicating the breed-specific feature of detected recombination events and the control of recombination events is a complex polygenic trait.

NixPb1-x nanowire arrays: effects of annealing.

Ni(x)Pb(1-x) nanowire arrays were successfully fabricated by AC electrodeposition within the nanopores of ordered porous alumina films prepared by a two-step anodization. Transmission electron microscopy analyses showed that the Ni-Pb nanoarrays are polycrystalline with dimension uniformity around 20 nm in diameter and lengths up to several micrometers. X-ray diffraction results revealed that the face-centered-cubic (fcc) Ni and fcc Pb peaks are detected when the Ni component (x) is below 0.71, indicating that the Ni(x)Pb(1-x) nanoarrays do not form metastable phase alloy. Hysteresis loops determined by vibrating sample magnetometer indicated that the Ni(x)Pb(1-x) nanoarrays obtained possess obvious magnetic anisotropy, and the perpendicular coercivity was lower than that of pure Ni nanowries before and after annealing. Annealing under magnetic field was carried out to examine the effect of a magnetic field on magnetic properties using an electromagnet field up to 0.3 T.

High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc.

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method-2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.

RADtyping: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations.

Genetic linkage maps are indispensable tools in genetic, genomic and breeding studies. As one of genotyping-by-sequencing methods, RAD-Seq (restriction-site associated DNA sequencing) has gained particular popularity for construction of high-density linkage maps. Current RAD analytical tools are being predominantly used for typing codominant markers. However, no genotyping algorithm has been developed for dominant markers (resulting from recognition site disruption). Given their abundance in eukaryotic genomes, utilization of dominant markers would greatly diminish the extensive sequencing effort required for large-scale marker development. In this study, we established, for the first time, a novel statistical framework for de novo dominant genotyping in mapping populations. An integrated package called RADtyping was developed by incorporating both de novo codominant and dominant genotyping algorithms. We demonstrated the superb performance of RADtyping in achieving remarkably high genotyping accuracy based on simulated and real mapping datasets. The RADtyping package is freely available at http://www2.ouc.edu.cn/mollusk/ detailen.asp?id=727.

Transcriptome sequencing of Zhikong scallop (Chlamys farreri) and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis).

BACKGROUND: Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops. RESULTS: In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected. CONCLUSION: Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.

Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).

BACKGROUND: Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus. RESULTS: In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome. CONCLUSION: Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.

Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX.

BACKGROUND: Bivalves comprise 30,000 extant species, constituting the second largest group of mollusks. However, limited genetic research has focused on this group of animals so far, which is, in part, due to the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bivalve research. In the present study, we performed de novo transcriptome sequencing to first produce a comprehensive expressed sequence tag (EST) dataset for the Yesso scallop (Patinopecten yessoensis). RESULTS: In a single 454 sequencing run, 805,330 reads were produced and then assembled into 32,590 contigs, with about six-fold sequencing coverage. A total of 25,237 unique protein-coding genes were identified from a variety of developmental stages and adult tissues based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified. More than 49,000 single nucleotide polymorphisms (SNPs) and 2,700 simple sequence repeats (SSRs) were also detected. CONCLUSION: Our data provide the most comprehensive transcriptomic resource currently available for P. yessoensis. Candidate genes potentially involved in growth, reproduction, and stress/immunity-response were identified, and are worthy of further investigation. A large number of SNPs and SSRs were also identified and ready for marker development. This resource should lay an important foundation for future genetic or genomic studies on this species.