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Frontiers of Agricultural Science and Engineering

  • Cover Illustration

    2017, Vol.4  No.3

    Rabies virus infection is always lethal and the virus has developed a series of strategies to evade host immune system. One of these strategies is keeping the integrity of blood brain barrier (BBB) by limiting the expression of inflammatory cytokines and chemokines. This picture shows how the BBB permeability is modulated by inflammatory cytokines and chemokines. This study reviews the important roles of cytokines and chemokines in antiviral innate immune [Detail] ...

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ISSN 2095-7505 (Print)
ISSN 2095-977X (Online)

Frontiers of Agricultural Science and Engineering has been added to Directory of Open Access Journals (DOAJ) on September 12, 2016.

This journal is a member of, and subscribes to the principles of, the Committee on Publication Ethics (COPE)

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, Volume 4 Issue 3 Previous Issue   
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EDITORIAL
Highlights of special issue on Animal Science
Jun REN
Front. Agr. Sci. Eng. . 2017, 4 (3): 257-259.   DOI: 10.15302/J-FASE-2017165
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REVIEW
Critical roles of chemokines and cytokines in antiviral innate immune responses during rabies virus infection
Ying HUANG, Clement Wesley GNANADURAI, Zhenfang FU
Front. Agr. Sci. Eng. . 2017, 4 (3): 260-267.   DOI: 10.15302/J-FASE-2016116
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The innate immune response is the first line of defense against viral invasion and pro-inflammatory chemokines and cytokines have a critical function in the innate immune responses against virus infections. The ability of a rabies virus (RABV) to induce the expression of chemokines and cytokines can lead to viral clearance from the central nervous system (CNS), whereas the ability to evade such expression and activation contributes to virulence and pathogenicity. In this review, the crucial contribution of chemokines/cytokines to clearing RABV from the CNS is discussed, including recruiting leukocytes into the CNS, enhancement of blood brain barrier permeability and activation of various immune cells that are essential for viral clearance. In addition, recombinant RABV expressing cytokines and chemokines can induce elevated innate and adaptive immune responses which result in clearing an established wild-type RABV infection in the CNS.

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Statistical considerations for genomic selection
Huimin KANG, Lei ZHOU, Jianfeng LIU
Front. Agr. Sci. Eng. . 2017, 4 (3): 268-278.   DOI: 10.15302/J-FASE-2017164
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Genomic selection is becoming increasingly important in animal and plant breeding, and is attracting greater attention for human disease risk prediction. This review covers the most commonly used statistical methods and some extensions of them, i.e., ridge regression and genomic best linear unbiased prediction, Bayesian alphabet, and least absolute shrinkage and selection operator. Then it discusses the measurement of the performance of genomic selection and factors affecting the prediction of performance. Among the measurements of prediction performance, the most important and commonly used measurement is prediction accuracy. In simulation studies where true breeding values are available, accuracy of genomic estimated breeding value can be calculated directly. In real or industrial data studies, either training-testing approach or k-fold cross-validation is commonly employed to validate methods. Factors influencing the accuracy of genomic selection include linkage disequilibrium between markers and quantitative trait loci, genetic architecture of the trait, and size and composition of the training population. Genomic selection has been implemented in the breeding programs of dairy cattle, beef cattle, pigs and poultry. Genomic selection in other species has also been intensively researched, and is likely to be implemented in the near future.

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Recent advances in understanding genetic variants associated with economically important traits in sheep (Ovis aries) revealed by high-throughput screening technologies
Song-Song XU, Meng-Hua LI
Front. Agr. Sci. Eng. . 2017, 4 (3): 279-288.   DOI: 10.15302/J-FASE-2017151
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Sheep are one of the most economically important domesticated animals for human society. However, genetic improvements for the key traits associated with meat, growth, milk, wool, reproduction, horns and tails progress slowly using conventional crossbreeding methods. With the development and utilization of high-throughput screening technologies over the last decade, a list of functional genes and genetic variants associated with these traits has been identified. This review covers recent genome-wide studies on sheep productive traits using high-throughput screening technologies, including those based on single-nucleotide polymorphisms and copy number variants at the whole-genome level (e.g., genome-wide association studies), transcriptome and DNA methylation sequences. Additionally, comprehensive information on functional genes and genetic variants associated with economically important traits in sheep is provided.

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Genomic regions under selection for important traits in domestic horse breeds
Xuexue LIU, Yuehui MA, Lin JIANG
Front. Agr. Sci. Eng. . 2017, 4 (3): 289-294.   DOI: 10.15302/J-FASE-2017155
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Horses were domesticated 5500 years ago, thousands of years later than other domestic animals; however, in this relatively short period, domestic horses have had a great impact on human history by accelerating civilization, revolutionizing warfare and advancing agricultural production. Modern breeding using marker-assisted selection has greatly accelerated breeding progress. Therefore, identification of genetic markers underlying the traits of interest in domestic horses is the basis for the modern breeding system. In this review, we present an overview of genetic mapping studies and genome wide analyses to identify the genomic regions targeted by positive selection for four important aspects of horses, coat color, racing performance, gait and height at withers. The MC1R locus, for example, has been shown to be the main gene responsible for chestnut color, and the MSTN locus has been shown to control the muscle fiber growth in racing breeds. The missense mutation in DMRT3 is the causal mutation for the alternate gaits in horses. Height at withers, a quantitative trait, was mapped to four major loci (3:105547002, 6:81481064, 9:75550059 and 11:232597 32) that can explain 83% of the height variations in domestic horses.

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The genetic regulation of skeletal muscle development: insights from chicken studies
Wen LUO, Bahareldin A. ABDALLA, Qinghua NIE, Xiquan ZHANG
Front. Agr. Sci. Eng. . 2017, 4 (3): 295-304.   DOI: 10.15302/J-FASE-2017159
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Skeletal muscle development is a complex multi-process trait regulated by various genetic factors. The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome, transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

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Genomics and genetic breeding in aquatic animals: progress and prospects
Wenteng XU, Songlin CHEN
Front. Agr. Sci. Eng. . 2017, 4 (3): 305-318.   DOI: 10.15302/J-FASE-2017154
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Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step, the expense of whole genome sequencing has been largely eliminated by the rapid updating of sequencing technology, leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. Multiple aquatic areas have been influenced by these findings, such as accelerated generation shift in the seed industry and the process of breeding improved lines. In this article, we have summarized the latest domestic and international progress of aquatic animals in nine aspects, including WGS and fine mapping, construction of high density genetic/physical maps, trait-related marker/genes screening, as well as sex control, genome editing, and other molecular breeding technologies. Finally, the existing problems in this field have been discussed and five future counter measures have been proposed accordingly.

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RESEARCH ARTICLE
Genome-wide analysis reveals selection for Chinese Rongchang pigs
Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI
Front. Agr. Sci. Eng. . 2017, 4 (3): 319-326.   DOI: 10.15302/J-FASE-2017161
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Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars, we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

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Genome-wide search for candidate genes determining vertebrae number in pigs
Longchao ZHANG, Jingwei YUE, Xin LIU, Jing LIANG, Kebin ZHAO, Hua YAN, Na LI, Lei PU, Yuebo ZHANG, Huibi SHI, Ligang WANG, Lixian WANG
Front. Agr. Sci. Eng. . 2017, 4 (3): 327-334.   DOI: 10.15302/J-FASE-2017163
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Longer porcine carcasses may be expected to have more vertebrae. Therefore, vertebrae number in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 578 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study (GWAS) identified 36 significant single nucleotide polymorphisms (SNPs) on the chromosomes SSC1 (294.28–300.32 Mb) and SSC7 (102.22–109.39 Mb). A 6.04-Mb region that contained all 13 significant SNPs on SSC1 also contained the gene NR6A1, previously reported to influence the number of vertebrae in pigs. However, the reported putative casual mutation of NR6A1 c.748C>T showed no genome-wide significant association with the trait, suggesting it was not a causal mutation in our population. The remaining 23 significant SNPs on SSC7 were concentrated in a 7.17-Mb region, which was within a quantitative trait locus interval for number of vertebrae. TMED10 was the closest gene to the most significant SNP and might be a candidate. Haplotype sharing and block analysis refined the QTL to an interval of about 3 Mb containing 29 candidate genes. Of these 29 genes, the previously reported possible casual mutation of VRTN g.19034A>C was not found to be a causal mutation in our population. Exploration of these genes via additional genetic and functional studies in mammals revealed that TGFβ3 could be a good candidate on SSC7. A mutation of TGFβ3 c.1749G>A was detected by GWAS and could be proposed as a candidate causal mutation, or as closely linked to a causal mutation, for the number of vertebrae in pigs.

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Genome-wide association analysis reveals genetic loci and candidate genes associated with intramuscular fat in Duroc pigs
Xingwang WANG, Rongrong DING, Jianping QUAN, Linxue YANG, Ming YANG, Enqin ZHENG, Dewu LIU, Gengyuan CAI, Zhenfang WU, Jie YANG
Front. Agr. Sci. Eng. . 2017, 4 (3): 335-341.   DOI: 10.15302/J-FASE-2017152
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Intramuscular fat (IMF) is a major meat-quality trait in pigs. The content of IMF is directly associated with the taste and flavor of pork. As a complex trait, there could be multiple genes affecting IMF content in pork. Genome-wide association study is a powerful tool to detect genomic regions associated with phenotypic variations. The objectives of the present study were to identify or refine the positions of genomic regions affecting IMF, and to characterize candidate genes and pathways that may influence this trait. Of note, we identified a significant region in longissium dorsi muscle in a Duroc pig population for IMF content with PorcineSNP60 v2 BeadChip. This region spans 1.24 Mb on chromosome 8 and had been identified as a quantitative trait locus for IMF in Pietrain, Large White, Landrace, and Leicoma pigs. In this region, eight SNPs were significantly associated with IMF content. Three genes proximal to these significant SNPs were considered candidate genes, including ZDHHC16, LOC102162218 and PCDH7. Our results confirm several previous findings and highlight several genes that may contribute to IMF variation in Duroc pigs.

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Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood
Haiyan WANG, Qiaoxia ZHANG, Lilin YIN, Xiangdong LIU, Shuhong ZHAO, Mengjin ZHU, Changchun LI
Front. Agr. Sci. Eng. . 2017, 4 (3): 342-352.   DOI: 10.15302/J-FASE-2017162
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Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes (DEGs) in extreme response (ER) pigs and 192 DEGs in moderate response (MR) pigs. Most DEGs were related to immune responses, included MXD1, CXCR4, CREG1, MyD88, CD14, TLR2, TLR4, IRF3 and IRF7. Gene ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation, immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals.

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Molecular authentication of the traditional Chinese medicine Tongren Dahuoluo Wan and its alternative formulation
Jikun WANG, Jing DU, Meng CAO, Lu YAO, Suhua XIE, Jiafu CHEN, Xingbo ZHAO
Front. Agr. Sci. Eng. . 2017, 4 (3): 353-357.   DOI: 10.15302/J-FASE-2017157
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Tongren Dahuoluo Wan has been a popular traditional Chinese medicine in international pharmaceutical markets for hundreds of years. Leopard bone powder is the key element in its formulation. However, the leopard has been listed for wildlife conservation, which limits the use of the leopard bone supplies. Therefore, an alternative formulation which substitutes leopard bone with zokor bone in the formula of Tongren Dahuoluo Wan is now manufactured. To develop a simple and reliable molecular method for authenticating the two patent medicines, mitochondrial nucleotide polymorphic sites of 12S rRNA, COI and Cytb genes were screened in leopard and zokor bones, and nine pairs of species-specific primers were verified for discriminating the two species. For the patent medicine authentication, we set up a molecular diagnostic assay to resolve the difficulties of low concentration of target DNAs and presence of PCR-inhibitory substances in this complex medicine, and successfully confirmed leopard or zokor content using the nine pairs of species-specific primers. We recommend a common technical strategy for authentication of species origins in traditional Chinese medicine, and discuss the experimental solutions for technical problems of molecular diagnostic assays.

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Conserved gene arrangement in the mitochondrial genomes of barklouse families Stenopsocidae and Psocidae
Xiaochen LIU, Hu LI, Yao CAI, Fan SONG, John-James WILSON, Wanzhi CAI
Front. Agr. Sci. Eng. . 2017, 4 (3): 358-365.   DOI: 10.15302/J-FASE-2017158
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Substantial variation in gene organization and arrangement has been reported for sequenced mitochondrial (mt) genomes from the suborders of the insect order Psocoptera. In this study we sequenced the complete mt genome of Stenopsocus immaculatus, the first representative of the family Stenopsocidae from the suborder Psocomorpha. Relative to the ancestral pattern, rearrangements of a protein-coding gene (nad3) and five tRNA genes (trnQ, trnC, trnN, trnS1, trnE) were found. This pattern was similar to that of two barklice from the family Psocidae, with the exception of the translocation of trnS1, trnE and trnI. Based on comparisons of pairwise breakpoint distances of gene rearrangements, gene number and chromosome number, it was concluded that mt genomes of Stenopsocidae and Psocidae share a relatively conserved pattern of gene rearrangements; mt genomes within the Psocomorpha have been generally stable over long evolutionary history; and mt gene rearrangement has been substantially faster in the booklice (suborder Troctomorpha) than in the barklice (suborders Trogiomorpha and Psocomorpha). It is speculated that the change of life history and persistence of unusual reproductive systems with maternal inheritance contributed to the contrasting rates in mt genome evolution between the barklice and booklice.

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Synthesis of haptens and production of antibodies to bisphenol A
Xiya ZHANG, Xiaoyun DONG, Sijun ZHAO, Yuebin KE, Kai WEN, Suxia ZHANG, Zhanhui WANG, Jianzhong SHEN
Front. Agr. Sci. Eng. . 2017, 4 (3): 366-372.   DOI: 10.15302/J-FASE-2017132
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Three immunizing haptens of bisphenol A (BPA), including two new haptens, were used to produce highly sensitive and specific polyclonal antibodies. The spacer arms of haptens for coupling to the protein carrier were located at different positions in BPA, and different length spacer arms were tested. Highly sensitive polyclonal antibodies were obtained and characterized using indirect competitive enzyme-linked immunosorbent assay (icELISA). Under optimized conditions, the half maximal inhibitory concentration (IC50) value of the best polyclonal antibody was 2.1 mg·L1, based on coating heterogeneous antigens, and this optimal polyclonal antibody was highly sensitive toward BPA and displayed negligible cross-reactivity with bisphenol B and bisphenol E. A sensitive icELISA method utilizing the polyclonal antibody was developed for the determination of BPA in milk. In spiked samples (5, 10 and 20mg·L1), the recovery ranged from 80% to 102% with a coefficient of variation (CV) value below 15.8%. The limit of detection of icELISA was 1.95mg·L1. These results indicate that the icELISA method is suitable for the detection of BPA in milk.

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