Frontiers of Agricultural Science and Engineering

ISSN 2095-7505 (Print)
ISSN 2095-977X (Online)
CN 10-1204/S
Postal Subscription Code 80-906

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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Approaches to achieve high grain yield and high resource use efficiency in rice
Jianchang YANG
Front. Agr. Sci. Eng.    2015, 2 (2): 115-123.
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This article discusses approaches to simultaneously increase grain yield and resource use efficiency in rice. Breeding nitrogen efficient cultivars without sacrificing rice yield potential, improving grain fill in later-flowering inferior spikelets and enhancing harvest index are three important approaches to achieving the dual goal of high grain yield and high resource use efficiency. Deeper root distribution and higher leaf photosynthetic N use efficiency at lower N rates could be used as selection criteria to develop N-efficient cultivars. Enhancing sink activity through increasing sugar-spikelet ratio at the heading time and enhancing the conversion efficiency from sucrose to starch though increasing the ratio of abscisic acid to ethylene in grains during grain fill could effectively improve grain fill in inferior spikelets. Several practices, such as post-anthesis controlled soil drying, an alternate wetting and moderate soil drying regime during the whole growing season, and non-flooded straw mulching cultivation, could substantially increase grain yield and water use efficiency, mainly via enhanced remobilization of stored carbon from vegetative tissues to grains and improved harvest index. Further research is needed to understand synergistic interaction between water and N on crop and soil and the mechanism underlying high resource use efficiency in high-yielding rice.

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One-step generation of myostatin gene knockout sheep via the CRISPR/Cas9 system
Hongbing HAN,Yonghe MA,Tao WANG,Ling LIAN,Xiuzhi TIAN,Rui HU,Shoulong DENG,Kongpan LI,Feng WANG,Ning LI,Guoshi LIU,Yaofeng ZHAO,Zhengxing LIAN
Front. Agr. Sci. Eng.    2014, 1 (1): 2-5.
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Initiation of Setaria as a model plant
Xianmin DIAO,James SCHNABLE,Jeffrey L. BENNETZEN,Jiayang LI
Front. Agr. Sci. Eng.    2014, 1 (1): 16-20.
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Model organisms such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have proven essential for efficient scientific discovery and development of new methods. With the diversity of plant lineages, some important processes such as C4 photosynthesis are not found in either Arabidopsis or rice, so new model species are needed. Due to their small diploid genomes, short life cycles, self-pollination, small adult statures and prolific seed production, domesticated foxtail millet (Setaria italica) and its wild ancestor, green foxtail (S. viridis), have recently been proposed as novel model species for functional genomics of the Panicoideae, especially for study of C4 photosynthesis. This review outlines the development of these species as model organisms, and discusses current challenges and future potential of a Setaria model.

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Recent advances in fruit crop genomics
Qiang XU,Chaoyang LIU,Manosh Kumar BISWAS,Zhiyong PAN,Xiuxin DENG
Front. Agr. Sci. Eng.    2014, 1 (1): 21-27.
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In recent years, dramatic progress has been made in the genomics of fruit crops. The publication of a dozen fruit crop genomes represents a milestone for both functional genomics and breeding programs in fruit crops. Rapid advances in high-throughput sequencing technology have revolutionized the manner and scale of genomics in fruit crops. Research on fruit crops is encompassing a wide range of biological questions which are unique and cannot be addressed in a model plant such as Arabidopsis. This review summarizes recent achievements of research on the genome, transcriptome, proteome, miRNAs and epigenome of fruit crops.

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Transcriptome analysis of wheat grain using RNA-Seq
Liu WEI,Zhihui WU,Yufeng ZHANG,Dandan GUO,Yuzhou XU,Weixia CHEN,Haiying ZHOU,Mingshan YOU,Baoyun LI
Front. Agr. Sci. Eng.    2014, 1 (3): 214-222.
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With the increase in consumer demand, wheat grain quality improvement has become a focus in China and worldwide. Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. In this study, two cDNA libraries from the developing grain and leaf-stem components of bread wheat cultivar, Nongda211, were sequenced using Roche/454 technology. There were 1061274 and 1516564 clean reads generated from grain and leaf-stem, respectively. A total of 61393 high-quality unigenes were obtained with an average length of 1456 bp after de novo assembly. The analysis of the 61393 unigenes involved in the biological processes of the grain showed that there were 7355 differentially expressed genes upregulated in the grain library. Gene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that many transcription products and transcription factors associated with carbohydrate and protein metabolism were abundantly expressed in the grain. These results contribute to excavate genes associated with wheat quality and further study how they interact.

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Fabrication of cellulose aerogel from wheat straw with strong absorptive capacity
Jian LI,Caichao WAN,Yun LU,Qingfeng SUN
Front. Agr. Sci. Eng.    2014, 1 (1): 46-52.
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An effectively mild solvent solution containing NaOH/PEG was employed to dissolve the cellulose extracted from the wheat straw. With further combined regeneration process and freeze-drying, the cellulose aerogel was successfully obtained. Scanning electron microscope, X-ray diffraction technique, Fourier transform infrared spectroscopy, and Brunauer-Emmett-Teller were used to characterize this cellulose aerogel of low density (about 40 mg·cm-3) and three-dimensional network with large specific surface area (about 101 m2·g-1). Additionally, with a hydrophobic modification by trimethylchlorosilane, the cellulose aerogel showed a strong absorptive capacity for oil and dye solutions.

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A review of hydrological/water-quality models
Liangliang GAO,Daoliang LI
Front. Agr. Sci. Eng.    2014, 1 (4): 267-276.
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Water quality models are important in predicting the changes in surface water quality for environmental management. A range of water quality models are wildly used, but every model has its advantages and limitations for specific situations. The aim of this review is to provide a guide to researcher for selecting a suitable water quality model. Eight well known water quality models were selected for this review: SWAT, WASP, QUALs, MIKE 11, HSPF, CE-QUAL-W2, ELCOM-CAEDYM and EFDC. Each model is described according to its intended use, development, simulation elements, basic principles and applicability (e.g., for rivers, lakes, and reservoirs and estuaries). Currently, the most important trends for future model development are: (1) combination models—individual models cannot completely solve the complex situations so combined models are needed to obtain the most appropriate results, (2) application of artificial intelligence and mechanistic models combined with non-mechanistic models will provide more accurate results because of the realistic parameters derived from non-mechanistic models, and (3) integration with remote sensing, geographical information and global position systems (3S) —3S can solve problems requiring large amounts of data.

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Foxtail millet: nutritional and eating quality, and prospects for genetic improvement
Lu HE,Bin ZHANG,Xingchun WANG,Hongying LI,Yuanhuai HAN
Front. Agr. Sci. Eng.    2015, 2 (2): 124-133.
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Foxtail millet is a minor yet important crop in some areas of the world, particularly northern China. It has strong adaptability to abiotic stresses, especially drought, and poor soil. It also has high nutritional value. Foxtail millet is rich in essential amino acids, fatty acids and minerals, and is considered to be one of the most digestible and non-allergenic grains available and has significant importance for human health. Given foxtail millet’s ability to adapt to abiotic stresses associated with climate change, it is more important than ever to develop breeding strategies that facilitate the increasing demand for high quality grain that better satisfies consumers. Here we review research on foxtail millet quality evaluation, appearance, cooking and eating quality at the phenotypic level. We review analysis of the main nutrients in foxtail millet, their relationships and the biochemical and genetic factors affecting their accumulation. In addition, we review past progress in breeding this regionally important crop, outline current status of breeding of foxtail millet, and make suggestions to improve grain quality.

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Managing nutrient for both food security and environmental sustainability in China: an experiment for the world
Fusuo ZHANG, Zhenling CUI, Weifeng ZHANG
Front. Agr. Sci. Eng.    2014, 1 (1): 53-61.
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The challenges of how to simultaneously ensure global food security, improve nitrogen use efficiency (NUE) and protect the environment have received increasing attention. However, the dominant agricultural paradigm still considers high yield and reducing environmental impacts to be in conflict with one another. Here we examine a Three-Step-Strategy of past 20 years to produce more with less in China, showing that tremendous progress has been made to reduce N fertilizer input without sacrificing crop yield. The first step is to use technology for in-season root-zone nutrient management to significantly increase NUE. The second is to use technology for integrated nutrient management to increase both yield and NUE by 15%–20%. The third step is to use technology for integrated soil-crop system management to increase yield and NUE by 30%–50% simultaneously. These advances can thus be considered an effective agricultural paradigm to ensure food security, while increasing NUE and improving environmental quality.

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Progress, problems and prospects of porcine pluripotent stem cells
Hanning WANG,Yangli PEI,Ning LI,Jianyong HAN
Front. Agr. Sci. Eng.    2014, 1 (1): 6-15.
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Pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced PSCs (iPSCs), can differentiate into cells of the three germ layers, suggesting that PSCs have great potential for basic developmental biology research and wide applications for clinical medicine. Genuine ESCs and iPSCs have been derived from mice and rats, but not from livestock such as the pig—an ideal animal model for studying human disease and regenerative medicine due to similarities with human physiologic processes. Efforts to derive porcine ESCs and iPSCs have not yielded high-quality PSCs that can produce chimeras with germline transmission. Thus, exploration of the unique porcine gene regulation network of preimplantation embryonic development may permit optimization of in vitro culture systems for raising porcine PSCs. Here we summarize the recent progress in porcine PSC generation as well as the problems encountered during this progress and we depict prospects for generating porcine naive PSCs.

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Comparative proteomic analysis of cold responsive proteins in two wheat cultivars with different tolerance to spring radiation frost
Shujuan ZHANG,Guoqi SONG,Yulian LI,Jie GAO,Jiao WANG,Guiju CHEN,Haosheng LI,Genying LI,Zhendong ZHAO
Front. Agr. Sci. Eng.    2014, 1 (1): 37-45.
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Spring radiation frost (SRF) is a severe environmental stress which impairs wheat yield and productivity worldwide. To better understand the mechanism of wheat (Triticum aestivum) responding to SRF, a comparative proteomic analysis was performed to analyze the changes of the key proteins in two wheat cultivars Jimai22 and Luyuan301 with high and low tolerance to SRF respectively. A total of 43 differentially expressed proteins (DEPs) which mainly involved in carbohydrate metabolism, amino acid metabolism, resistance proteins and antioxidant enzymes, photosynthesis and cellular respiration proteins, cell-wall related proteins, protein translation/processing/degradation and signal transduction were isolated and identified by two-dimensional electrophoresis and MALDI-TOF-TOF MS. The results revealed that of the 21 DEPs in Jimai22 responding to the SRF, 13 DEPs were upregulated and 8 DEPs were downregulated, and that of the 22 DEPs in Luyuan301, 9 DEPs were upregulated and 13 DEPs were downregulated. These DEPs might be responsible for the stronger cold resistance of Jimai22 compared to Luyuan301. The expression pattern and function analysis of these DEPs were very significant to understanding the mechanism of the SRF responses in wheat.

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Transcriptome resources and genome-wide marker development for Japanese larch (Larix kaempferi)
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
Front. Agr. Sci. Eng.    2014, 1 (1): 77-84.
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While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of Larix kaempferi, a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old L. kaempferi trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from Larix embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of Larix.

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Prevention and control of zoonoses at their source: from the Chinese perspective
Songtao YANG,Yuwei GAO,Jun QIAN,Quan LIU,Xuexing ZHENG,Hualei WANG,Zhiping XIA,Xianzhu XIA
Front. Agr. Sci. Eng.    2014, 1 (2): 96-103.
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Zoonoses are a significant public health concern and cause considerable socioeconomic problems globally. The emergence of severe acute respiratory syndrome (SARS), highly pathogenic avian influenza (HPAI), and Ebola virus disease (EVD) has had a significant effect on the national economy and public health in China, and other countries. This review analyzed zoonotic disease issues faced by China, and the main factors contributing to the risk of zoonotic disease. The Chinese government has devised new strategies and has taken measures to deal with the challenges of these diseases, and the prevention and control of zoonoses at their source. A strategy that is suited to China’s national conditions, is proposed.

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Review of the direct thermochemical conversion of lignocellulosic biomass for liquid fuels
Jianchun JIANG,Junming XU,Zhanqian SONG
Front. Agr. Sci. Eng.    2015, 2 (1): 13-27.
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Increased demand for liquid transportation fuels, environmental concerns and depletion of petroleum resources requires the development of efficient conversion technologies for production of second-generation biofuels from non-food resources. Thermochemical approaches hold great potential for conversion of lignocellulosic biomass into liquid fuels. Direct thermochemical processes convert biomass into liquid fuels in one step using heat and catalysts and have many advantages over indirect and biological processes, such as greater feedstock flexibility, integrated conversion of whole biomass, and lower operation costs. Several direct thermochemical processes are employed in the production of liquid biofuels depending on the nature of the feedstock properties: such as fast pyrolysis/liquefaction of lignocellulosic biomass for bio-oil, including upgrading methods, such as catalytic cracking and hydrogenation. Owing to the substantial amount of liquid fuels consumed by vehicular transport, converting biomass into drop-in liquid fuels may reduce the dependence of the fuel market on petroleum-based fuel products. In this review, we also summarize recent progress in technologies for large-scale equipment for direct thermochemical conversion. We focus on the technical aspects critical to commercialization of the technologies for production of liquid fuels from biomass, including feedstock type, cracking catalysts, catalytic cracking mechanisms, catalytic reactors, and biofuel properties. We also discuss future prospects for direct thermochemical conversion in biorefineries for the production of high grade biofuels.

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China’s new problems of food security revealed by the Food Equivalent Unit
Huilong LIN,Ruichao LI,Cangyu JIN,Chong WANG,Maohong WEI,Jizhou REN
Front. Agr. Sci. Eng.    2014, 1 (1): 69-76.
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China's food security has a great influence on the world, and has always been the top priority in China. In recent years, as the concept of food security is evolving into one of nutrition security and the importance of food diversity is increasing, research based on nutrition security and broad food systems are increasingly needed in today’s China. Thus, not only grain for human consumption, but also animal foods have been integrated into the Food Equivalent, which is used to analyze China’s current agriculture system and reveal the water resource distribution. The results indicated that the average animal food consumption has risen by 78.6%, and now China’s daily supply of animal food per capita has reached about 50% of that in the USA and 80% of that in the South Korea. So there exist an obvious disparity in animal food supply between China and these two countries. It is impossible for the China’s current agricultural system to achieve the level in the USA. Under China’s current agricultural system, the consumption proportion of feed grain had surpassed the consumption of food grain, increased sharply from 33% in 1992 to 67% in 2011. However, the growth potential of total grain output is approaching an upper limit, so the continued growth of feed grain demand exerts great pressure on the China’s food supply. The discordance of the spatial distribution of water resource and virtual water revealed that China’s current agriculture system had a low efficiency in being able to achieve food and nutrition security. China’s current “grain farming” cannot meet the demand of increasing nutrition and appropriate resource utilization. The implementation of grassland agriculture appears feasible and necessary for saving feed grain, providing a large number of high-quality animal foods and appropriate water resource utilization.

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Oocyte-associated transcription factors in reprogramming after somatic cell nuclear transfer: a review
Fengxia YIN,Hui LIU,Shorgan BOU,Guangpeng LI
Front. Agr. Sci. Eng.    2014, 1 (2): 104-113.
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Oocytes are unique cells with the inherent capability to reprogram nuclei. The reprogramming of the somatic nucleus from its original cellular state to a totipotent state is essential for term development after somatic cell nuclear transfer. The nuclear-associated factors contained within oocytes are critical for normal fertilization by sperm or for somatic cell nuclear reprogramming. The chromatin of somatic nuclei can be reprogrammed by factors in the egg cytoplasm whose natural function is to reprogram sperm chromatin. The oocyte first obtains its reprogramming capability in the early fetal follicle, and then its capacity is enriched in the late growth phase and reaches its highest capability for reprogramming as fully-grown germinal vesicle oocytes. The cytoplasmic milieu most likely contains all of the specific transcription and/or reprogramming factors necessary for cellular reprogramming. Certain transcription factors in the cytoplast may be critical as has been demonstrated for induced pluripotent stem cells. The maternal pronucleus exerts a predominant, transcription-dependent effect on embryo cytofragmentation, with a lesser effect imposed by the ooplasm and the paternal pronucleus. With deep analysis of transcriptomics in oocytes and early developmental stage embryos more maternal transcription factors inducing cellular reprogramming will be identified.

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Progress on major genes for high fecundity in ewes
Qiuyue LIU,Zhangyuan PAN,Xiangyu WANG,Wenping HU,Ran DI,Yaxing YAO,Mingxing CHU
Front. Agr. Sci. Eng.    2014, 1 (4): 282-290.
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The existence of major genes affecting fecundity in sheep flocks throughout the world has been demonstrated. Three major genes whose mutations can increase ovulation rate have been discovered, and all related to the transforming growth factor β (TGF-β) superfamily. The mutant FecB of bone morphogenetic protein receptor 1B (BMPR1B) has an additive effect on ovulation rate. Six mutations (FecXI, FecXH, FecXG, FecXB, FecXL, FecXR) of bone morphogenetic protein 15 (BMP15) related with fertility have been identified that share the same mechanism. All the mutants can increase ovulation rate in heterozygotes and cause complete sterility in homozygotes. Homozygous ewes with two new mutations (FecXGr, FecXO) of BMP15 had increased ovulation rate without causing sterility. There are five mutations in growth differentiation factor 9 (GDF9) associated with sheep prolificacy where FecGE and FecGF have additive an effect on ovulation rate and litter size. The newly identified β-1,4-N-acetylgalactosaminyltransferase 2 (B4GALNT2) gene of FecL is proposed as a new mechanism of ovulation rate regulation in sheep. Woodlands is an X-linked maternally imprinted gene which increases ovulation rate. In addition, several putative major genes need to be verified. This review is focused on the identification of the mutations and mechanisms whereby the major genes affecting ovulation rate.

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A post-GWAS replication study confirming the association of C1<?Pub Caret?>4H8orf33 gene with milk production traits in dairy cattle
Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN
Front. Agr. Sci. Eng.    2014, 1 (4): 321-330.
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Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population. Of these, 38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition. By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis, 26 genes were found to contain or be near to such SNPs. Among them, the C14H8orf33 gene is merely 87 bp away from the significant SNP, Hapmap30383-BTC-005848. Hence, we report herein genotype-phenotype associations to further validate the genetic effects of the C14H8orf33 gene. By pooled DNA sequencing of 14 unrelated Holstein sires, a total of 18 with seven novel SNPs were identified. Among them, nine SNPs were in the 5′ regulatory region, one in exon 6 and the other in the 3′ UTR and 3′ regulatory region. A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population. The results showed that these SNPs were statistically significant for more than two traits [P<(0.0001-0.0267)]. In addition, mRNA expression analyses revealed that C14H8orf33 was ubiquitous in eight different tissues, with a relatively higher expression level in the mammary gland than in other tissues. These findings, therefore, provide strong evidence for association of C14H8orf33 variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

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Advances in crop phenotyping and multi-environment trials
Zhe LIU,Fan ZHANG,Qin MA,Dong AN,Lin LI,Xiaodong ZHANG,Dehai ZHU,Shaoming LI
Front. Agr. Sci. Eng.    2015, 2 (1): 28-37.
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Efficient evaluation of crop phenotypes is a prerequisite for breeding, cultivar adoption, genomics and phenomics study. Plant genotyping is developing rapidly through the use of high-throughput sequencing techniques, while plant phenotyping has lagged far behind and it has become the rate-limiting factor in genetics, large-scale breeding and development of new cultivars. In this paper, we consider crop phenotyping technology under three categories. The first is high-throughput phenotyping techniques in controlled environments such as greenhouses or specifically designed platforms. The second is a phenotypic strengthening test in semi-controlled environments, especially for traits that are difficult to be tested in multi-environment trials (MET), such as lodging, drought and disease resistance. The third is MET in uncontrolled environments, in which crop plants are managed according to farmer’s cultural practices. Research and application of these phenotyping techniques are reviewed and methods for MET improvement proposed.

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Lodging resistance and yield potential of winter wheat: effect of planting density and genotype
Yonggui XIAO,Jianjun LIU,Haosheng LI,Xinyou CAO,Xianchun XIA,Zhonghu HE
Front. Agr. Sci. Eng.    2015, 2 (2): 168-178.
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Improved lodging resistance is important for achieving high yield in irrigated environments. This study was conducted to determine genotypic variation in lodging resistance and related morphological traits among winter wheat cultivars planted at two densities, and to identify key traits associated with lodging resistance. Lodging performance of 28 genotypes, including 24 released cultivars and four advanced lines, was evaluated at 250 plants per square meter and 500 plants per square meter in Shandong province during the 2008&ndash;2009 and 2009&ndash;2010 crop seasons. At the higher density, the average grain yield was 2.6% higher, even though lodging score rose by as much as 136%. The higher planting density increased lodging through increased leaf area index (LAI), plant height, center of gravity and length of basal internodes, and reduced grain weight per spike and diameter of the lower two stem internodes. LAI, center of gravity and diameter of first internodes, as the important indicators for lodging resistance, were significantly correlated with lodging score, with R= 0.62, 0.59 and &minus;0.52 (P<0.01), respectively. Plant pushing resistance was significantly associated with diameter and length of the first internodes (R = 0.71&ndash;0.77, P<0.01), indicating it could be used to assess the strength of the lower stem. Higher planting density could be used to select genotypes with lodging resistance in irrigated environments. Cultivars carrying high plant density tolerance and high yield potential, such as Jimai 22 and Liangxing 66, were recommended as leading cultivars for production as well as elite crossing parents for further increasing yield potential in the Yellow and Huai Valleys Winter Wheat Zone in China.

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Estimating the effect of urease inhibitor on rice yield based on NDVI at key growth stages
Kailou LIU,Yazhen LI,Huiwen HU
Front. Agr. Sci. Eng.    2014, 1 (2): 150-157.
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The effect of the urease inhibitor, N-(n-butyl) thiophosphoric triamide (NBPT) at a range of application rates on rice production was examined in a field experiment at Jinxian County, Jiangxi Province, China. The normalized difference vegetation index (NDVI) was measured at key growth stages in both early and late rice. The results showed that the grain yield increased significantly when urea was applied with NBPT, with the highest yield observed at 1.00% NBPT (wt/wt). NDVI differed with the growth stage of rice; it remained steady from the heading to the filling stage. Rice yield could be predicted from the NDVI taken at key rice growing stages, with R2 ranging from 0.34 to 0.69 in early rice and 0.49 to 0.70 in late rice. The validation test showed that RMSE (t·hm-2) values were 0.77 and 0.87 in early and late rice, respectively. Therefore, it was feasible to estimate rice yield for different amounts of urease inhibitor using NDVI.

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Genomics approaches to unlock the high yield potential of cassava, a tropical model plant
Shengkui ZHANG,Ping’an MA,Haiyan WANG,Cheng LU,Xin CHEN,Zhiqiang XIA,Meiling ZOU,Xinchen ZHOU,Wenquan WANG
Front. Agr. Sci. Eng.    2014, 1 (4): 259-266.
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Cassava, a tropical food, feed and biofuel crop, has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition, which makes it highly suitable as a model plant for tropical crops. However, the understanding of the metabolism and genomics of this important crop is limited. The recent breakthroughs in the genomics of cassava, including whole-genome sequencing and transcriptome analysis, as well as advances in the biology of photosynthesis, starch biosynthesis, adaptation to drought and high temperature, and resistance to virus and bacterial diseases, are reviewed here. Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars. Finally, the current challenges and future potential of cassava as a model plant are discussed.

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Genomic regions associated with the sex-linked inhibitor of dermal melanin in Silkie chicken
Ming TIAN,Rui HAO,Suyun FANG,Yanqiang WANG,Xiaorong GU,Chungang FENG,Xiaoxiang HU,Ning LI
Front. Agr. Sci. Eng.    2014, 1 (3): 242-249.
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A unique characteristic of the Silkie chicken is its fibromelanosis phenotype. The dermal layer of its skin, its connective tissue and shank dermis are hyperpigmented. This dermal hyperpigmentation phenotype is controlled by the sex-linked inhibitor of dermal melanin gene (ID) and the dominant fibromelanosis allele. This study attempted to confirm the genomic region associated with ID. By genotyping, ID was found to be closely linked to the region between GGA_rs16127903 and GGA_rs14685542 (8406919 bp) on chromosome Z, which contains ten functional genes. The expression of these genes was characterized in the embryo and 4 days after hatching and it was concluded that MTAP, encoding methylthioadenosinephosphorylase, would be the most likely candidate gene. Finally, target DNA capture and sequence analysis was performed, but no specific SNP(s) was found in the targeted region of the Silkie genome. Further work is necessary to identify the causal ID mutation located on chromosome Z.

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Plant genetic engineering and genetically modified crop breeding: history and current status
Xingchun WANG,Shujun CHANG,Jie LU,Rupert FRAY,Don GRIERSON,Yuanhuai HAN
Front. Agr. Sci. Eng.    2017, 4 (1): 5-27.
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This review charts the major developments in the genetic manipulation of plant cells that have taken place since the first gene transfer experiments using Ti plasmids in 1983. Tremendous progress has been made in both our scientific understanding and technological capabilities since the first genetically modified (GM) crops were developed with single gene resistances to herbicides, insects, viruses, and the silencing of unde-sirable genes. Despite opposition in some parts of the world, the area planted with first generation GM crops has grown from 1.7 Mhm2 in 1996 to 179.7 Mhm2 hectares in 2015. The toolkit available for genetic modification has expanded greatly since 1996 and recently Nobel Laureates have called on Greenpeace to end their blanket opposition, and plant scientists have urged that consideration be given to the benefits of GM crops based on actual evidence. It is now possible to use GM to breed new crop cultivars resistant to a much wider range of pests and diseases, and to produce crops better able to adapt to climate change. The advent of new CRISPR-based technologies makes it possible to contemplate a much wider range of improvements based on transfer of new metabolic pathways and traits to improve nutritional quality, with a much greater degree of precision. Use of GM, sometimes in conjunction with other approaches, offers great opportunities for improving food quality, safety, and security in a changing world.

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Effects of DNA damage on oocyte meiotic maturation and early embryonic development
Shen YIN,Junyu MA,Wei SHEN
Front. Agr. Sci. Eng.    2014, 1 (3): 185-190.
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DNA damage is one of the most common threats to meiotic cells. It has the potential to induce infertility and genetic abnormalities that may be passed to the embryo. Here, we reviewed exogenous factors which could induce DNA damage. Specially, we addressed the different effects of DNA damage on mouse oocytes and embryonic development. Complex DNA damage, double-strand breaks, represents a more difficult repair process and involves various repair pathways. Understanding the mechanisms involved in DNA damage responses may improve therapeutic strategies for ovarian cancer and fertility preservation.

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Assessment of vaccination strategies against highly pathogenic avian influenza in China
Honglei SUN,Jinhua LIU
Front. Agr. Sci. Eng.    2014, 1 (4): 277-281.
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Vaccination for highly pathogenic avian influenza (HPAI) has been implemented in China for a decade, however, the virus is still present in poultry. A series of recombinant vaccines, Re-1 to Re-7, have been developed and used, and Re-8 will also be used in clinical settings to prevent the prevailing flu strains. The question remains, when can China eradicate the disease? Here, we review the epidemiology of H5 HPAI along with the development, usage and problems of vaccines. Further suggestions for controlling the disease in China are provided.

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Expression of recombinant human butyrylcholinesterase in the milk of transgenic mice
Dan LU,Shengzhe SHANG,Shen LIU,Ying WU,Fangfang WU,Tan TAN,Qiuyan LI,Yunping DAI,Xiaoxiang HU,Yaofeng ZHAO,Ning LI
Front. Agr. Sci. Eng.    2014, 1 (3): 179-184.
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Butyrylcholinesterase (BCHE) is a natural bioscavenger that protects humans against organophosphate toxicity. Due to the limited yield of human BCHE (hBCHE) when purifying from human plasma, it is necessary to find an alternative method to produce this protein. One potential method is to produce transgenic livestock that make modified milk containing high concentration of hBCHE. In this study, we cloned the hBCHEgene into a human lactoferrin (hLF) bacterial artificial chromosome (BAC) construct to make a hLF-hBCHE BAC construct. Subsequently, we injected the BAC construct into pronuclei of mouse fertilized embryos and generated transgenic mice. Expression analysis showed that recombinant hBCHE (rhBCHE) was expressed efficiently in the mammary gland of the transgenic mice and the concentration of rhBCHE in the milk of individual mice ranged from 76±12 to 159±28 mg·L-1. Protein function tests showed that rhBCHE has the same enzymatic activity as the native hBCHE. Our results pave the way for making transgenic livestock to produce large quantities of rhBCHE.

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Characterization of NDM-1-producing carbapenemase in Acinetobacter spp. and E. coli isolates from diseased pigs
Rongmin ZHANG,Yang WANG,Zhihai LIU,Jiyun LI,Wenjuan YIN,Lei LEI,Congming WU,Jianzhong SHEN
Front. Agr. Sci. Eng.    2015, 2 (3): 223-229.
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In recent years, the mobile metallo-β-lactamase (MBL) genes have been found to correspond to one of the most important resistance characters identified in Gram-negative bacteria, severely affecting clinical chemotherapy and threatening public health. The prevalence of mobile MBL genes and their flanking regions in Gram-negative bacteria from diseased pigs in China was investigated. A total of 334 lung samples from diseased pigs were screened for Gram-negative bacteria classified as non-susceptible to meropenem (MIC≥4 mg·L−1). Six isolates, including three Escherichia coli, two Acinetobacter baumanii and one A. calcoaeticus, exhibited MBL production and carried the blaNDM-1 gene. S1-PFGE and Southern blot analysis showed that the blaNDM-1 gene was located on the chromosome of one A. baumanii isolate and on plasmids of various sizes in the other five isolates. MIC testing using broth microdilution revealed that all blaNDM-1-carrying isolates and some of their transconjugants exhibited resistance to almost all β-lactams tested. Whole genome sequencing revealed that the flanking region of the blaNDM-1 gene from all porcine isolates had high levels of similarity with the corresponding regions in human isolates. One porcine E. coli isolate carrying blaNDM-1 was typed as ST48, a common sequence type in human E. coli isolates. These results suggest the possibility of human-to-food animal transfer of blaNDM-1-producing E. coli, highlighting the need for surveillance of carbapenemase producers among bacteria from food animals. In addition, the prudent use of antimicrobial agents to decrease the opportunities for co-selection of carbapenemase genes in food animals is also urgently needed.

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Inverted duplication including Endothelin 3 closely related to dermal hyperpigmentation in Silkie chickens
Ming TIAN,Suyun FANG,Yanqiang WANG,Xiaorong GU,Chungang FENG,Rui HAO,Xiaoxiang HU,Ning LI
Front. Agr. Sci. Eng.    2014, 1 (2): 121-129.
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The dermal hyperpigmentation phenotype in chickens is controlled by the dominant fibromelanosis allele. One of the ten unique characteristics of Silkie chickens is the fibromelanosis phenotype, which is pigmentation in the dermal layer of the skin and connective tissue. In this study, we found a mutation of fibromelanosis, a genomic rearrangement that included an inverted duplication of endothelin3 (EDN3), is responsible. We show that, as a stimulator of melanoblast proliferation, EDN3 expression was increased in silkie embryos and in both skin and muscle throughout adulthood. EDN3 expression led to an increase in expression of the downstream genes EDNRB2 and TYRP2, and was closely relate with the hyperpigmentation phenotype. We examined eight different Chinese chicken breeds showing hyperpigmentation and conclude that this structural genetic variant exists in all fibromelanosis chicken breeds.

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Management strategies of marine food resources under multiple stressors with particular reference of the Yellow Sea large marine ecosystem
Qisheng TANG
Front. Agr. Sci. Eng.    2014, 1 (1): 85-90.
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In this study two main management strategies are discussed: one is to develop resource conservation-based capture fisheries, and the other is to develop environmentally friendly aquaculture. During the resource recovery period, the development of environmentally friendly aquaculture should be encouraged, especially in integrated multi-trophic aquaculture, which is adaptive, efficient and sustainable. For future development and better understanding the ecosystem, it is necessary to further strengthen basic research.

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