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Identification of two novel linear epitopes on the p30 protein of African swine fever virus
YU Si-hui, SHAN Zhao-meng, YANG Jing-jing, LIU Yi-ning, WU Chang-de, ZHANG Zhen-jiang, ZHU Yuan-mao, MENG Bo, ZHAN Jia-xing, WEN Xue-xia, ZHANG Ying
2023, 22 (6): 1945-1949.   DOI: 10.1016/j.jia.2023.04.012
Abstract233)      PDF in ScienceDirect      
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Effect of dioscorea opposite waste on growth performance, blood parameters, rumen fermentation and rumen bacterial community in weaned lambs
GUO Yun-xia, YANG Ruo-chen, DUAN Chun-hui, WANG Yong, HAO Qing-hong, JI Shou-kun, YAN Hui, ZHANG Ying-jie, LIU Yue-qin
2023, 22 (6): 1833-1846.   DOI: 10.1016/j.jia.2022.10.002
Abstract292)      PDF in ScienceDirect      

This study investigated the effects of dioscorea opposite waste (DOW) on the growth performance, blood parameters, rumen fermentation and rumen microbiota of weaned lambs.  Sixty healthy weaned Small-Tailed Han lambs (male, (22.68±2.56) kg initially) were used as the experimental animals.  Four levels of concentrate: 0 (control, CON), 10% (DOW1), 15% (DOW2) and 20% (DOW3), were replaced with DOW in the basal diet as experimental treatments.  The results showed that lambs fed the DOW2 diet had a higher (P<0.05) dry matter intake (DMI) than the other groups.  There was no significant difference (P>0.05) among DOW groups in average daily weight gain (ADG), and replacing concentrate with DOW linearly or quadratically increased (P<0.05) the ADG, while lambs fed the DOW2 diet showed greater (P<0.05) ADG than the CON group.  The relative plasma concentration of growth hormone (GH), insulin like growth factor-1 (IGF-1) and insulin were affected by DOW, replacing concentrate with DOW linearly or quadratically (P<0.05) enhanced the plasma concentration of GH, IGF-1 and insulin, which was significantly higher (P<0.05) in the DOW2 group than in the CON, DOW1 and DOW3 groups.  In addition, the DOW treatment showed a lower (P<0.05) concentration of blood urea nitrogen (BUN) than the CON group.  Replacing concentrate with DOW quadratically decreased (P<0.05) the ruminal ammonia nitrogen (NH3-N) and increased (P<0.05) the total of volatile fatty acids (TVFAs) at 0 and 4 h after feeding as well as linearly decreased (P<0.05) the NH3-N at 8 h after feeding.  Replacing concentrate with DOW linearly decreased (P<0.05) the propionate and increased the aceate before feeding, and linearly decreased (P<0.05) propionate and quadratically increased (P<0.05) the aceate at 4 and 8 h after feeding.  Lambs fed the DOW2 diet increased the phylum Firmicutes and genera Succiniclasticum and Ruminococcus_1 groups, whereas decreased (P<0.05) the relative abundance of phylum Deferribacteres and genera intestinimonas and Ruminiclostridium.  In summary, replacing the concentrate with 15% DOW was beneficial for improving the rumen fermentation and ADG by increasing the DMI and modulating the rumen microbial community.

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The succession of fecal bacterial community and its correlation with the changes of serum immune indicators in lambs from birth to 4 months
YIN Xue-jiao, JI Shou-kun, DUAN Chun-hui, TIAN Pei-zhi, JU Si-si, YAN Hui, ZHANG Ying-jie, LIU Yue-qin
2023, 22 (2): 537-550.   DOI: 10.1016/j.jia.2022.08.055
Abstract215)      PDF in ScienceDirect      

Early bacterial colonization and succession within the gastrointestinal tract have been suggested to be crucial in the development of host immunity.  In this study, we have investigated the changes in live weight and concentrations of selected serum parameters in relation to their fecal bacterial communities as determined by high throughput sequencing of the 16S rRNA gene over the same period in lambs.  The results showed that lambs’ growth performance, the serum parameters, fecal bacterial community and fecal bacterial functions were all affected (P<0.05) by age of the lambs.  Similarity within age groups of fecal microbiota was lower in the preweaning period and increased sharply (P<0.05) after weaning at 60 days.  The similarity between the samples collected from birth to 90 days of age and those collected at 120 days of age, increased (P<0.05) sharply after 30 days of age.  Some age-associated changes in microbial genera were correlated with the changes in concentrations of immune indicators, including negative (P<0.05) correlations between the relative abundance of Lachnospiraceae UCG-010, Eubacterium coprostanoligenes group, Ruminococcaceae UCG-005, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminiclostridium 6, Ruminococcaceae UCG-008, and Oscillibacter with serum concentrations of lipopolysaccharide (LPS), D-lactate dehydrogenase (DLA), immunoglobulin (IgA, IgM, and IgG), and cytokines (interleukin-1β (IL-1β), IL-6, IL-12, and IL-17), tumor necrosis factor-α (TNF-α), and the relative abundance of these genera increased from 45 days of age.  In conclusion, these results suggested that the age-related abundances of particular genera were correlated with serum markers of immunity in lambs, and there might be a critical window in the period from birth to 45 days of age which provide an opportunity for potential manipulation of the fecal microbial ecosystems to enhance immune function.

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The metabolomics variations among rice, brown rice, wet germinated brown rice, and processed wet germinated brown rice

REN Chuan-ying, LU Shu-wen, GUAN Li-jun, HONG Bin, ZHANG Ying-lei, HUANG Wen-gong, LI Bo, LIU Wei, LU Wei-hong
2022, 21 (9): 2767-2776.   DOI: 10.1016/j.jia.2022.07.025
Abstract178)      PDF in ScienceDirect      

Germination and processing are always accompanied by significant changes in the metabolic compositions of rice.  In this study, polished rice (rice), brown rice, wet germinated brown rice (WGBR), high temperature and pressure-treated WGBR (WGBR-HTP), and low temperature-treated WGBR (WGBR-T18) were enrolled.  An untargeted metabolomics assay isolated 6 122 positive ions and 4 224 negative ions (multiple difference ≥1.2 or ≤0.8333, P<0.05, and VIP≥1) by liquid chromatography-mass spectrum.  These identified ions were mainly classified into three categories, including the compounds with biological roles, lipids, and phytochemical compounds.  In addition to WGBR-T18 vs. WGBR, massive differential positive and negative ions were revealed between rice of different forms.  Flavonoids, fatty acids, carboxylic acids, and organoxygen compounds were the dominant differential metabolites.  Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, there 7 metabolic pathways (phenylalanine/tyrosine/tryptophan biosynthesis, histidine metabolism, betalain biosynthesis, C5-branched dibasic acid metabolism, purine metabolism, zeatin biosynthesis, and carbon metabolism) were determined between brown rice and rice.  Germination changed the metabolic pathways of porphyrin and chlorophyll, pyrimidine, and purine metabolisms in brown rice.  In addition, phosphonate and phosphinate metabolism, and arachidonic acid metabolism were differential metabolic pathways between WGBR-HTP and WGBR-T18.  To sum up, there were obvious variations in metabolic compositions of rice, brown rice, WGBR, and WGBR-HTP.  The changes of specific metabolites, such as flavonoids contributed to the anti-oxidant, anti-inflammatory, anti-cancer, and immunomodulatory effects of GBR.  HTP may further improve the nutrition and storage of GBR through influencing specific metabolites, such as flavonoids and fatty acids.

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An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits
ZHANG Ying, CAO Yu-fen, HUO Hong-liang, XU Jia-yu, TIAN Lu-ming, DONG Xing-guang, QI Dan, LIU Chao
2022, 21 (8): 2275-2290.   DOI: 10.1016/S2095-3119(21)63885-6
Abstract261)      PDF in ScienceDirect      

Germplasm resources are an important basis for genetic breeding and analysis of complex traits, and research on genetic diversity is conducive to the exploration and creation of new types of germplasm.  In this study, the distribution frequency, coefficient of variation, Shannon–Wiener index, and variance and cluster analyses were used to analyze the diversity and trait differences of 39 fruit phenotypic traits from 570 pear accessions, which included 456 pear accessions from 11 species and 114 interspecific hybrid cultivars that had been stored in the National Germplasm Repository of Apple and Pear (Xingcheng, China).  The comprehensive evaluation indices were screened by correlation, principal component and regression analyses.  A total of 132 variant types were detected in 28 categorical traits of pear germplasm fruit, which indicate a rich diversity.  The diversity indices in decreasing order were: fruit shape (1.949), attitude of calyx (1.908), flesh texture type (1.700), persistency of calyx (1.681), russet location (1.658), relief of area around eye basin (1.644), flavor (1.610) and ground color (1.592).  The coefficient of variation of titratable acidity in the 11 numerical traits of pear germplasm fruit was as high as 128.43%, which could more effectively reflect the differences between pear accessions.  The phenotypic differentiation coefficient Vst (66.4%) among the five cultivated pear species, including Pyrus bretschneideri (White Pear), Ppyrifolia (Sand Pear), Pussuriensis (Ussurian Pear), Psinkiangensis (Xinjiang Pear), and Pcommunis (European Pear), was higher than the within population phenotypic differentiation coefficient Vst (33.6%).  The variation among populations was the main source of variation in pear fruit traits.  A hierarchical cluster analysis divided the 389 accessions of six cultivated pear species, including Ppashia (Himalayan Pear), into six categories.  There were certain characteristics within the populations, and the differences between populations were not completely clustered by region.  For example, Sand Pear cultivars from Japan and the Korean Peninsula clustered together with those from China.  Most of the White Pear cultivars clustered with the Sand Pear, and a few clustered with the Ussurian Pear cultivars.  The Ussurian Pear and European Pear cultivars clustered separately.  The Xinjiang Pear and Himalayan Pear did not cluster together, and neither did the cultivars.  Seventeen traits, three describing fruit weight and edible rate (fruit diameter, fruit length and fruit core size), five describing outer quality and morphological characteristics (over color, amount of russeting, dot obviousness, fruit shape, and stalk length), and nine describing inner quality (flesh color, juiciness of flesh, aroma, flavor, flesh texture, flesh texture type, soluble solid contents, titratable acidity, and eating quality) were selected from the 39 traits by principal component and stepwise regression analyses.  These 17 traits could reflect 99.3% of the total variation and can be used as a comprehensive evaluation index for pear germplasm resources.

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Establishment and application of an SNP molecular identification system for grape cultivars
WANG Fu-qiang, FAN Xiu-cai, ZHANG Ying, SUN Lei, LIU Chong-huai, JIANG Jian-fu
2022, 21 (4): 1044-1057.   DOI: 10.1016/S2095-3119(21)63654-7
Abstract228)      PDF in ScienceDirect      
We aimed to develop a set of single nucleotide polymorphism (SNP) markers that can be used to distinguish the main cultivated grape (Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection.  A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions using specific locus amplified fragment sequencing, of which 442 were successfully designed as Kompetitive Allele Specific PCR (KASP) markers.  A set of 27 markers that completely distinguishes 304 sequenced grape accessions was determined by using the program, and 26 effective markers were screened based on 23 representative grape cultivars.  Finally, a total of 46 out of 48 KASP markers, including 22 markers selected by the research group in the early stage, were re-screened based on 348 grape accessions.  Population structure, principal component, and cluster analyses all showed that the 348 grape accessions were best divided into two populations.  In addition, cluster analysis subdivided them into six subpopulations.  According to genetic distance, V. labrusca, V. davidii, V. heyneana, and V. amurensis were far from V. vinifera, while V. vinifera×V. labrusca and V. amurensis×V. vinifera were somewhere in between these two groups.  Furthermore, a core set of 25 KASP markers could distinguish 95.69% of the 348 grape accessions, and the other 21 markers were used as extended markers.  Therefore, SNP molecular markers based on KASP typing technology provide a new way for mapping DNA fingerprints in grape cultivars.  With high efficiency and accuracy and low cost, this technology is more competitive than other current identification methods.  It also has excellent application prospects in the grape distinctness, uniformity, and stability (DUS) test, as well as in promoting market rights protection in the near future.

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Dynamic change of fungal community in the gastrointestinal tract of growing lambs
YIN Xue-jiao, JI Shou-kun, DUAN Chun-hui, TIAN Pei-zhi, JU Si-si, YAN Hui, ZHANG Ying-jie, LIU Yue-qin
2022, 21 (11): 3314-3328.   DOI: 10.1016/j.jia.2022.08.092
Abstract249)      PDF in ScienceDirect      

Although fungal communities in the gastrointestinal tract have a significant role in animal health and performance, their dynamics within the tract are not well known.  Thus, this study investigated fungal community dynamics in the rumen and rectum of lambs from birth to 4 mon of age by using IT1S rDNA sequencing technology together with the RandomForest approach to determine age-related changes in the fungal ecology.  The results indicated that gastrointestinal fungal community composition, diversity, and abundance altered (P<0.05) with the increasing age of the lambs.  Two phyla, Ascomycota and Basidiomycota, dominated the samples.  Similarity within age groups of the rumen fungi increased sharply after 45 days of age, while the similarity increased (P<0.05) significantly after 60 days of age in the rectum.  The age-related genera, Acremonium, Microascus, Valsonectria, Myrmecridium, Scopulariopsis, Myrothecium, Saccharomyces, and Stephanonectria, were presented in both ruminal and rectal communities, and their changes in relative abundance were consistent at both sites.  The principal coordinates analysis showed significant differences (P<0.05) between the fungal communities in the rumen and rectum.  Our findings demonstrate that both the age of lambs and the gastrointestinal tract region can affect the composition of these fungal communities, and this provides new insight and directions for future studies in this research area.

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Development of a cELISA for effective detection of the antibody against H7 subtype of avian influenza virus
WANG Cong-cong, WANG Si-wen, ZHANG Ying, SHI Jian-zhong, YIN Xin, LI Cheng-jun, WANG Xiu-rong
2022, 21 (1): 199-207.   DOI: 10.1016/S2095-3119(21)63645-6
Abstract167)      PDF in ScienceDirect      
H7 avian influenza viruses (AIVs) normally circulated among birds before.  From 1996 to 2012, human infections with H7 AIVs (H7N2, H7N3, and H7N7) were reported in Canada, Italy, Mexico, the Netherlands, the United Kingdom and the USA.  Until March 2013, human infections with H7N9 AIVs were reported in China.  Since then, H7N9 AIVs have continued to circulate in both humans and birds.  Therefore, the detection of antibodies against the H7 subtype of AIVs has become an important topic.  In this study, a competitive enzyme-linked immunosorbent assay (cELISA) method for the detection of antibody against H7 AIVs was established.  The optimal concentration of antigen coating was 5 μg mL–1, serum dilution was 1/10, and enzyme-labeled antibody was 1/3 000.  To determine the cut-off value of cELISA, percent inhibition (PI) was determined by using receiver operating characteristic (ROC) curve analysis in 178 AIVs negative samples and 368 AIVs positive serum samples (n=546).  When PI was set at 40%, the specificity and sensitivity of cELISA were 99.4 and 98.9%, respectively.  This method could detect the antibodies against H7Nx (N1–N4, N7–N9) AIVs, and showed no reaction with AIVs of H1–H6 and H8–H15 subtypes or common avian viruses such as Newcastle disease virus (NDV), Infectious bronchitis virus (IBV) and Infectious bursal disease virus (IBDV), exhibiting good specificity.  This method showed a coincidence rate of 98.56% with hemagglutinin inhibition (HI) test.  And the repeatability experiment revealed that the coefficients of variation (CV) of intra- and inter-batch repetition were all less than 12%.  The data indicated that the cELISA antibody-detection method established in this study provided a simple and accurate technical support for the detection of a large number of antibody samples of H7-AIV.
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Improving winter wheat grain yield and water-/nitrogen-use efficiency by optimizing the micro-sprinkling irrigation amount and nitrogen application rate
LI Jin-peng, ZHANG Zhen, YAO Chun-sheng, LIU Yang, WANG Zhi-min, FANG Bao-ting, ZHANG Ying-hua
2021, 20 (2): 606-621.   DOI: 10.1016/S2095-3119(20)63407-4
Abstract174)      PDF in ScienceDirect      
Available irrigation resources are becoming increasingly scarce in the North China Plain (NCP), and nitrogen-use efficiency of crop production is also relatively low. Thus, it is imperative to improve the water-use efficiency (WUE) and nitrogen fertilizer productivity on the NCP. Here, we conducted a two-year field experiment to explore the effects of different irrigation amounts (S60, 60 mm; S90, 90 mm; S120, 120 mm; S150, 150 mm) and nitrogen application rates (150, 195 and 240 kg ha–1; denoted as N1, N2 and N3, respectively) under micro-sprinkling with water and nitrogen combined on the grain yield (GY), yield components, leaf area index (LAI), flag leaf chlorophyll content, dry matter accumulation (DM), WUE, and nitrogen partial factor productivity (NPFP). The results indicated that the GY and NPFP increased significantly with increasing irrigation amount, but there was no significant difference between S120 and S150; WUE significantly increased first but then decreased with increasing irrigation and S120 achieved the highest WUE. The increase in nitrogen was beneficial to improving the GY and WUE in S60 and S90, while the excessive nitrogen application (N3) significantly reduced the GY and WUE in S120 and S150 compared with those in the N2 treatment. The NPFP significantly decreased with increasing nitrogen rate under the same irrigation treatments. The synchronous increase in spike number (SN) and 1 000-grain weight (TWG) was the main reason for the large increase in GY by micro-sprinkling with increasing irrigation, and the differences in SN and TGW between S120 and S150 were small. Under S60 and S90, the TGW increased with increasing nitrogen application, which enhanced the GY, while N2 achieved the highest TWG in S120 and S150. At the filling stage, the LAI increased with increasing irrigation, and greater amounts of irrigation significantly increased the chlorophyll content in the flag leaf, which was instrumental in increasing DM after anthesis and increasing the TGW. Micro-sprinkling with increased amounts of irrigation or excessive nitrogen application decreased the WUE mainly due to the increase in total water consumption (ET) and the small increase or decrease in GY. Moreover, the increase in irrigation increased the total nitrogen accumulation or contents (TNC) of plants at maturity and reduced the residual nitrate-nitrogen in the soil (SNC), which was conducive to the increase in NPFP, but there was no significant difference in TNC between S120 and S150. Under the same irrigation treatments, an increase in nitrogen application significantly increased the residual SNC and decreased the NPFP. Overall, micro-sprinkling with 120 mm of irrigation and a total nitrogen application of 195 kg ha–1 can lead to increases in GY, WUE and NPFP on the NCP.
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In situ measurements of winter wheat diurnal changes in photosynthesis and environmental factors reveal new insight into photosynthesis improvement by super-high-yield cultivation
MA Ming-yang, LIU Yang, ZHANG Yao-wen, QIN Wei-long, WANG Zhi-min, ZHANG Ying-hua, LU Cong-ming, LU Qing-tao
2021, 20 (2): 527-539.   DOI: 10.1016/S2095-3119(20)63554-7
Abstract120)      PDF in ScienceDirect      
In past 30 years, the wheat yield per unit area of China has increased by 79%. The super-high-yield (SH) cultivation played an important role in improving the wheat photosynthesis and yield. In order to find the ecophysiological mechanism underneath the high photosynthesis of SH cultivation, in situ diurnal changes in the photosynthetic gas exchange and chlorophyll (Chl) a fluorescence of field-grown wheat plants during the grain-filling stage and environmental factors were investigated. During the late grain-filling stage at 24 days after anthesis (DAA), the diurnal changes in net CO2 assimilation rate were higher under SH treatment than under high-yield (H) treatment. From 8 to 24 DAA, the actual quantum yield of photosystem II (PSII) electron transport in the light-adapted state (ΦPSII) in the flag leaves at noon under SH treatment were significantly higher than those under H treatment. The leaf temperature, soil temperature and soil moisture were better suited for higher rates of leaf photosynthesis under SH treatment than those under H treatment at noon. Such diurnal changes in environmental factors in wheat fields could be one of the mechanisms for the higher biomass and yield under SH cultivation than those under H cultivation. ΦPSII and CO2 exchange rate in wheat flag leaves under SH and H treatments had a linear correlation which could provide new insight to evaluate the wheat photosynthesis performance under different conditions.
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Identification and gene mapping of the starch accumulation and premature leaf senescence mutant ossac4 in rice
ZHU Mao-di, CHEN Xin-long, ZHU Xiao-yan, XING Ya-di, DU Dan, ZHANG Ying-ying, LIU Ming-ming, ZHANG Qiu-li, LU Xin, PENG Sha-sha, HE Guang-hua, ZHANG Tian-quan
2020, 19 (9): 2150-2164.   DOI: 10.1016/S2095-3119(19)62814-5
Abstract140)      PDF in ScienceDirect      
The rice mutant ossac4 (starch accumulating 4) was raised from seeds of the rice (Oryza sativa L.) indica maintainer line Xinong 1B treated with ethyl methanesulfonate.  The distal and medial portions of the second leaf displayed premature senescence in the ossac4 mutant at the four-leaf stage.  Physiological and biochemical analysis, and cytological examination revealed that the ossac4 mutant exhibited the premature leaf senescence phenotype.  At the four-leaf stage, the leaves of the ossac4 mutant exhibited significantly increased contents of starch compared with those of the wild type (WT).  Quantitative real-time PCR analysis showed that the expression levels of photosynthesis-associated genes were down-regulated and the expression levels of glucose metabolism-associated genes were abnormal.  Genetic analysis indicated that the ossac4 mutation was controlled by a single recessive nuclear gene.  The OsSAC4 gene was localized to a 322.7-kb interval between the simple-sequence repeat marker XYH11-90 and the single-nucleotide polymorphism marker SNP5300 on chromosome 11.  The target interval contained 20 annotated genes.  The present results demonstrated that ossac4 represents a novel starch accumulation and premature leaf senescence mutant, and lays the foundation for cloning and functional analysis of OsSAC4.
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Mapping and genetic validation of a grain size QTL qGS7.1 in rice (Oryza sativa L.)
XUE Pao1, ZHANG Ying-xin1, LOU Xiang-yang1, ZHU Ai-ke, CHEN Yu-yu, SUN Bin, YU Ping, CHENG Shi-hua, CAO Li-yong, ZHAN Xiao-deng
2019, 18 (8): 1838-1850.   DOI: 10.1016/S2095-3119(18)62113-6
Abstract202)      PDF in ScienceDirect      
Grain size is a major determinant of grain weight, which is one of the components of rice yield.  The objective o this study was to identify novel, and important quantitative trait loci (QTLs) for grain size and weight in rice.  QTLs were mapped using a BC4F4 population including 192 backcross inbred lines (BILs) derived from a backcross between Xiaolijing (XLJ) and recombinant inbred lines (RILs).  The mapping population was planted in both Lingshui (Hainan, 2015) and Fuyang (Zhejiang, 2016), with the short- and long-day conditions, respectively.  A total of 10 QTLs for grain length, four for grain width, four for the ratio of grain length to width, and 11 for grain weight were detected in at least one environment and were distributed across 11 chromosomes.  The phenotypic variance explained ranged from 6.76–25.68%, 14.30–34.03%, 5.28–26.50%, and 3.01–22.87% for grain length, grain width, the ratio of grain length to width, and thousand grain weight, respectively.  Using the sequential residual heterozygotes (SeqRHs) method, qGS7.1, a QTL for grain size and weight, was mapped in a 3.2-Mb interval on chromosome 7.  No QTLs about grain size and weight were reported in previous studies in this region, providing a good candidate for functional analysis and breeding utilization.
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Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism
WANG Jing-lu, ZHANG Ying, PAN Xiao-di, DU Jian-jun, MA Li-ming, GUO Xin-yu
2019, 18 (2): 350-360.   DOI: 10.1016/S2095-3119(18)62029-5
Abstract290)      PDF (1658KB)(274)      
Maize (Zea mays L.) yield depends not only on the conversion and accumulation of carbohydrates in kernels, but also on the supply of carbohydrates by leaves.  However, the carbon metabolism process in leaves can vary across different leaf regions and during the day and night.  Hence, we used Weighted Gene Co-expression Network analysis (WGCNA) with the gene expression profiles of carbon metabolism to identify the modules and genes that may associate with particular regions in a leaf and time of day.  There were a total of 45 samples of maize leaves that were taken from three different regions of a growing maize leaf at five time points.  Robust Multi-array Average analysis was used to pre-process the raw data of GSE85963 (accession number), and quality control of data was based on Pearson correlation coefficients.  We obtained eight co-expression network modules.  The modules with the highest significance of association with LeafRegion and TimePoint were selected.  Functional enrichment and gene-gene interaction analyses were conducted to acquire the hub genes and pathways in these significant modules.  These results can support the findings of similar studies by providing evidence of potential module genes and enriched pathways associated with leaf development in maize.
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Influence of lactic acid bacteria, cellulase, cellulase-producing Bacillus pumilus and their combinations on alfalfa silage quality
LI Dong-xia, NI Kui-kui, ZHANG Ying-chao, LIN Yan-li, YANG Fu-yu
2018, 17 (12): 2768-2782.   DOI: 10.1016/S2095-3119(18)62060-X
Abstract290)      PDF in ScienceDirect      
This study assessed the effects of lactic acid bacteria (LAB), cellulase, cellulase-producing Bacillus pumilus and their combinations on the fermentation characteristics, chemical composition, bacterial community and in vitro digestibility of alfalfa silage.  A completely randomized design involving a 8 (silage additives)×3 or 2 (silage days) factorial arrangement of treatments was adopted in the present study.  The 8 silage additive treatments were: untreated alfalfa (control); two commercial additives (GFJ and Chikuso-1); an originally selected LAB (Lactobacillus plantarum a214) isolated from alfalfa silage; a cellulase-producing Bacillus (CB) isolated from fresh alfalfa; cellulase (C); and the combined additives (a214+C and a214+CB).  Silage fermentation characteristics, chemical composition and microorganism populations were analysed after 30, 60 and 65 days (60 days followed by exposure to air for five additional days).  In vitro digestibility was analysed for 30 and 60 days.  Compared with the other treatments, selected LAB a214, a214 combined with either C or CB, and Chikuso-1 had the decreased (P<0.001) pH and increased (P<0.001) lactic acid concentrations during the ensiling process, and there were no differences (P>0.05) among them.  Fiber degradation was not significant (P≥0.054) in any C or CB treatments.  The a214 treatment showed the highest (P=0.009) in vitro digestibility of dry matter (595.0 g kg–1 DM) after ensiling and the highest abundance of Lactobacillus (69.42 and 79.81%, respectively) on days 60 and 65, compared to all of other treatments.  Overall, the silage quality of alfalfa was improved with the addition of a214, which indicates its potential as an alfalfa silage inoculant.
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A simulation of winter wheat crop responses to irrigation management using CERES-Wheat model in the North China Plain
ZHOU Li-li, LIAO Shu-hua, WANG Zhi-min, WANG Pu, ZHANG Ying-hua, YAN Hai-jun, GAO Zhen, SHEN Si, LIANG Xiao-gui, WANG Jia-hui, ZHOU Shun-li
2018, 17 (05): 1181-1193.   DOI: 10.1016/S2095-3119(17)61818-5
Abstract540)      PDF (1260KB)(256)      
To improve efficiency in the use of water resources in water-limited environments such as the North China Plain (NCP), where winter wheat is a major and groundwater-consuming crop, the application of water-saving irrigation strategies must be considered as a method for the sustainable development of water resources.  The initial objective of this study was to evaluate and validate the ability of the CERES-Wheat model simulation to predict the winter wheat grain yield, biomass yield and water use efficiency (WUE) responses to different irrigation management methods in the NCP.  The results from evaluation and validation analyses were compared to observed data from 8 field experiments, and the results indicated that the model can accurately predict these parameters.  The modified CERES-Wheat model was then used to simulate the development and growth of winter wheat under different irrigation treatments ranging from rainfed to four irrigation applications (full irrigation) using historical weather data from crop seasons over 33 years (1981–2014).  The data were classified into three types according to seasonal precipitation: <100 mm, 100–140 mm, and >140 mm.  Our results showed that the grain and biomass yield, harvest index (HI) and WUE responses to irrigation management were influenced by precipitation among years, whereby yield increased with higher precipitation.  Scenario simulation analysis also showed that two irrigation applications of 75 mm each at the jointing stage and anthesis stage (T3) resulted in the highest grain yield and WUE among the irrigation treatments.  Meanwhile, productivity in this treatment remained stable through different precipitation levels among years.  One irrigation at the jointing stage (T1) improved grain yield compared to the rainfed treatment and resulted in yield values near those of T3, especially when precipitation was higher.  These results indicate that T3 is the most suitable irrigation strategy under variable precipitation regimes for stable yield of winter wheat with maximum water savings in the NCP.  The application of one irrigation at the jointing stage may also serve as an alternative irrigation strategy for further reducing irrigation for sustainable water resources management in this area.
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Conditional and unconditional QTLs mapping of gluten strength in common wheat (Triticum aestivum L.)
LIU Tong-tong, LIU Kai, WANG Fang-fang, ZHANG Ying, LI Qing-fang, ZHANG Kai-ran, XIE Chu-peng, TIAN Ji-chun, CHEN Jian-sheng
2017, 16 (10): 2145-2155.   DOI: 10.1016/S2095-3119(16)61564-2
Abstract707)      PDF in ScienceDirect      
    Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantitative trait loci (QTLs) analysis for gluten strength, as measured by sedimentation volume (SV) and gluten index (GI), was performed using the QTLNetwork 2.0 software. Recombinant inbred lines (RILs) derived from the winter wheat varieties Shannong 01-35×Gaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identified using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15–45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals: WPT-3743–GLU-D1 (1D), WPT-7001–WMC258 (1B), and WPT-8682–WPT-5562 (1B). Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs (QGi1D-13 and QSv1D-14) and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.
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Development of a real-time RT-PCR method for the detection of newly emerged highly pathogenic H7N9 influenza viruses
WANG Xiu-rong, GU Lin-lin, SHI Jian-zhong, XU Hai-feng, ZHANG Ying, ZENG Xian-ying, DENG Guo-hua, LI Cheng-jun, CHEN Hua-lan
2017, 16 (09): 2055-2061.   DOI: 10.1016/S2095-3119(17)61655-1
Abstract837)      PDF in ScienceDirect      
   In 2013, a human influenza outbreak caused by a novel H7N9 virus occurred in China.  Recently, the H7N9 virus acquired multiple basic amino acids at its hemagglutinin (HA) cleavage site, leading to the emergence of a highly pathogenic virus.  The development of an effective diagnostic method is imperative for the prevention and control of highly pathogenic H7N9 influenza.  Here, we designed and synthesized three pairs of primers based on the nucleotide sequence at the HA cleavage site of the newly emerged highly pathogenic H7N9 influenza virus.  One of the primer pairs and the corresponding probe displayed a high level of amplification efficiency on which a real-time RT-PCR method was established.  Amplification using this method resulted in a fluorescent signal for only the highly pathogenic H7N9 virus, and not for any of the H1–H15 subtype reference strains, thus demonstrating high specificity.  The method detected as low as 39.1 copies of HA-positive plasmid and exhibited similar sensitivity to the virus isolation method using embryonated chicken eggs.  Importantly, the real-time RT-PCR method exhibited 100% consistency with the virus isolation method in the diagnosis of field samples.  Collectively, our data demonstrate that this real-time RT-PCR assay is a rapid, sensitive and specific method, and the application will greatly aid the surveillance, prevention, and control of highly pathogenic H7N9 influenza viruses.
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Genetic mapping of quantitative trait loci for the stigma exsertion rate in rice (Oryza sativa L.)
Md Habibur Rahman, ZHANG Ying-xin, SUN Lian-ping, ZHANG Ke-qin, Md Sazzadur Rahman, WU Wei-xun, ZHAN Xiao-deng, CAO Li-yong, CHENG Shi-hua
2017, 16 (07): 1423-1431.   DOI: 10.1016/S2095-3119(16)61540-X
Abstract1026)      PDF in ScienceDirect      
    The efficiency of hybrid rice seed production can be improved by increasing the percentage of exserted stigmas. To identify quantitative trait loci (QTLs) for this trait, we conducted QTL mapping using 75 chromosome segment substitution lines (CSSLs) developed from a cross between the donor parent, Xieqingzao B (XQZB), a maintainer line which has high stigma exsertion and the recurrent parent, Zhonghui 9308 (ZH9308), a restorer line which has low stigma exsertion. A total of nine QTLs (qSSE5, qSSE10, qSSE11, qDSE10, qDSE11, qTSE5, qTSE6, qTSE10, and qTSE11) for single stigma exsertion (SSE), dual stigma exsertion (DSE) and total stigma exsertion (TSE) were assessed in two environments (Hainan and Zhejiang). Six of these QTLs (qSSE10, qSSE11, qDSE10, qDSE11, qTSE10, and qTSE11) were found in both environments, while one QTL (qTSE6) was found in only Hainan, and two QTLs (qSSE5 and qTSE5) were found in only Zhejiang. The qSSE10, qSSE11, qDSE10, qDSE11, qTSE6, qTSE10, and qTSE11 alleles, which are derived from the parent XQZB, exhibited a positive additive effect. In contrast, the qSSE5 and qTSE5 alleles, which are derived from the parent ZH9308, exhibited a negative additive effect. The SSE, DSE and TSE traits were significantly correlated with each other in an environmentally dependent manner. These results indicated that the lines showing higher values for SSE were more likely to exhibit increased values for DSE, which would ultimately increase TSE. To evaluate the advantage of exserted stigmas for cross-pollination, single, dual and total stigma exsertion should be considered separately in future attempts at genetic improvement to achieve increased production of rice hybrid seeds. This study also provides information for fine mapping, gene cloning and particularly marker-assisted selection (MAS), on the latter and with an emphasis the phenotypic effects and implications of the QTLs for practical use in hybrid rice breeding.
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The renewability and quality of shallow groundwater in Sanjiang and Songnen Plain, Northeast China
ZHANG Bing, SONG Xian-fang, ZHANG Ying-hua, HAN Dong-mei, TANG Chang-yuan, YANG Li-hu, WANG Zhong-liang
2017, 16 (01): 229-238.   DOI: 10.1016/S2095-3119(16)61349-7
Abstract1085)      PDF in ScienceDirect      
Groundwater is a key component for water resources in Sanjiang and Songnen Plain, an important agriculture basement in China.  The quality and the renewability of irrigation groundwater are essential for the stock raising and agricultural production.  Shallow groundwater was sampled and analyzed for various variables.  The salinity sodium concentration and bicarbonate hazard, were examined with regard to the United States Department of Agriculture (USDA) irrigation water standards.  The concentration of chlorofluorocarbons (CFCs) was determined to analyze the age of groundwater.  Most groundwater samples labeled as excellent to good for irrigation with low salinity hazard or medium salinity hazard.  Four groundwater samples were good and suspected for irrigation with high salinity hazard.  Generally groundwater in Sanjiang Plain was younger than the groundwater in Songnen Plain.  Meanwhile, groundwater nearby river is younger than the groundwater further away inside the watershed.  The mean age of groundwater in Sanjiang Plain is in average of 44.1, 47.9 and 32.8 years by CFC-11 (CCl3F), CFC-12 (CCl2F2) and CFC-113 (C2Cl3F3),  respectively.  The mean ages of groundwater in Songnen Plain is in average of 46.1, 53.4, and 40.7 years by CFC-11, CFC-12 and CFC-113, respectively.  Thus, groundwater nearby rivers could be directly exploited as irrigation water.  Partial groundwater has to be processed to lower the salt concentration rather than directly utilized as irrigation water in Songnen Plain.  Both water quality and renewability should be put in mind for sustainable agricultural development and water resources management.
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Isolation, identification, derivatization and phytotoxic activity of secondary metabolites produced by Cladosporium oxysporum DH14, a locust-associated fungus
LU Yi-hui, LI Shuai, SHAO Ming-wei, XIAO Xiao-hui, KONG Li-chun, JIANG Dong-hua, ZHANG Ying-lao
2016, 15 (4): 832-839.   DOI: 10.1016/S2095-3119(15)61145-5
Abstract1975)      PDF in ScienceDirect      
Three main phytotoxic compounds including lunatoic acid A (1), 5Z-7-oxozeaenol (2) and zeaenol (3) were isolated from the fermentation broth of Cladosporium oxysporum DH14, a fungus residing in the locust (Oxya chinensis ) gut.  Two additional derivative compounds, compound 1a and 1b, were synthesized by methylation and chlorination of compound 1, respectively.  The structures of such compounds were identified on the basis of spectroscopic analysis and by comparison of the corresponding data to those previously reported in the literature.  Compounds 1–3 exhibited significantly phytotoxic activities against the radicle growth of Amaranthus retroflexus L. with the 50% inhibitory concentrations (IC50 values) of 4.51, 4.80 and 8.16 μg mL–1, respectively, which is comparable to that positive control 2,4-dichlorophenoxyacetic acid (IC50=1.95 μg mL–1).  Furthermore, the compound 1 showed selective phytotoxic activity with the inhibition rate of less than 22% against the crops of Brassica rapa L., Sorghum durra, Brassica campestris L., Capsicum annucm and Raphanus sativus L. under the concentration of 100 μg mL–1.  Both derivatives of compound 1 had moderate phytotoxic activity against the radicle growth of A. retroflexus L.  The findings of our present study suggest that these compounds provide new promising candidates for the potential management strategies of weeds.
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Contribution of ear photosynthesis to grain yield under rainfed and irrigation conditions for winter wheat cultivars released in the past 30 years in North China Plain
WANG Yun-qi, XI Wen-xing, WANG Zhi-min, WANG Bin, XU Xue-xin, HAN Mei-kun, ZHOU Shun-li, ZHANG Ying-hua
2016, 15 (10): 2247-2256.   DOI: 10.1016/S2095-3119(16)61408-9
Abstract1673)           
    To understand the contribution of ear photosynthesis to grain yield and its response to water supply in the improvement of winter wheat, 15 cultivars released from 1980 to 2012 in North China Plain (NCP) were planted under rainfed and irrigated conditions from 2011 to 2013, and the ear photosynthesis was tested by ear shading. During the past 30 years, grain yield significantly increased, the flag leaf area slightly increased under irrigated condition but decreased significantly under rainfed condition, the ratio of grain weight:leaf area significantly increased, and the contribution of ear photosynthesis to grain yield changed from 33.6 to 64.5% and from 32.2 to 57.2% under rainfed and irrigated conditions, respectively. Grain yield, yield components, and ratio of grain weight:leaf area were positively related with contribution of ear photosynthesis. The increase in grain yield in winter wheat was related with improvement in ear photosynthesis contribution in NCP, especially under rainfed condition.
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Programmed cell death, antioxidant response and oxidative stress in wheat flag leaves induced by chemical hybridization agent SQ-1
WANG Shu-ping, ZHANG Gai-sheng, SONG Qi-lu, ZHANG Ying-xin, LI Ying, GUO Jia-lin, CHEN Zheng, NIU Na, MA Shou-cai, WANG Jun-wei
2016, 15 (1): 76-86.   DOI: 10.1016/S2095-3119(14)60977-1
Abstract2101)      PDF in ScienceDirect      
Male sterility induced by a chemical hybridization agent (CHA) is an important tool for utilizing crop heterosis. Leaves, especially the flag leaves, as CHA initial recipients play a decisive role in inducing male sterility. To investigate effects of different treatment times of CHA-SQ-1 used, morphological, biochemical and physiological responses of wheat flag leaves were detected in this study. CHA induced programmed cell death (PCD) as shown in terminal deoxynucleotidyl transferase-mediated dUTP nick end-labelling (TUNEL) and DNA laddering analysis. In the early phase, CHA-SQ-1 triggered organelle changes and PCD in wheat leaves accompanied by excess production of reactive oxygen species (O2 -. and H2O2) and down-regulation of the activities of superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POD). Meanwhile, leaf cell DNAs showed ladder-like patterns on agarose gel, indicating that CHA-SQ-1 led to the activation of the responsible endonuclease. The oxidative stress assays showed that lipid peroxidation was strongly activated and photosynthesis was obviously inhibited in SQ-1-induced leaves. However, CHA contents in wheat leaves gradually reduced along with the time CHA-SQ-1 applied. Young flags returned to an oxidative/antioxidative balance and ultimately developed into mature green leaves. These results provide explanation of the relations between PCD and anther abortion and practical application of CHA for hybrid breeding.
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Effect of nitrogen fertilization on yield, N content, and nitrogen fixation of alfalfa and smooth bromegrass grown alone or in mixture in greenhouse pots
XIE Kai-yun, LI Xiang-lin, HE Feng, ZHANG Ying-jun, WAN Li-qiang, David B Hannaway, WANG Dong, QIN Yan, Gamal M A Fadul
2015, 14 (9): 1864-1876.   DOI: 10.1016/S2095-3119(15)61150-9
Abstract1981)      PDF in ScienceDirect      
Planting grass and legume mixtures on improved grasslands has the potential advantage of realizing both higher yields and lower environmental pollution by optimizing the balance between applied N fertilizer and the natural process of legume biological nitrogen fixation. However, the optimal level of N fertilization for grass-legume mixtures, to obtain the highest yield, quality, and contribution of N2 fixation, varies with species. A greenhouse pot experiment was conducted to study the temporal dynamics of N2 fixation of alfalfa (Medicago sativa L.) grown alone and in mixture with smooth bromegrass (Bromus inermis Leyss.) in response to the addition of fertilizer N. Three levels of N (0, 75, and 150 kg ha–1) were examined using 15N-labeled urea to evaluate N2 fixation via the 15N isotope dilution method. Treatments were designated N0 (0.001 g per pot), N75 (1.07 g per pot) and N150 (2.14 g per pot). Alfalfa grown alone did not benefit from the addition of fertilizer N; dry matter was not significantly increased. In contrast, dry weight and N content of smooth bromegrass grown alone was increased significantly by N application. When grown as a mixture, smooth bromegrass biomass was increased significantly by N application, resulted in a decrease in alfalfa biomass. In addition, individual alfalfa plant dry weight (shoots+roots) was significantly lower in the mixture than when grown alone at all N levels. Smooth bromegrass shoot and root dry weight were significantly higher when grown with alfalfa than when grown alone, regardless of N application level. When grown alone, alfalfa’s N2 fixation was reduced with N fertilization (R2=0.9376, P=0.0057). When grown in a mixture with smooth bromegrass, with 75 kg ha–1 of N fertilizer, the percentage of atmospheric N2 fixation contribution to total N in alfalfa (%Ndfa) had a maximum of 84.07 and 83.05% in the 2nd and 3rd harvests, respectively. Total 3-harvest %Ndfa was higher when alfalfa was grown in a mixture than when grown alone (shoots: |t|=3.39, P=0.0096; root: |t|=3.57, P=0.0073). We believe this was due to smooth bromegrass being better able to absorb available soil N (due to its fibrous root system), resulting in lower soil N availability and allowing alfalfa to develop an effective N2 fixing symbiosis prior to the 1st harvest. Once soil N levels were depleted, alfalfa was able to fix N2, resulting in the majority of its tissue N being derived from biological nitrogen fixation (BNF) in the 2nd and 3rd harvests. When grown in a mixture, with added N, alfalfa established an effective symbiosis earlier than when grown alone; in monoculture BNF did not contribute a significant portion of plant N in the N75 and N150 treatments, whereas in the mixture, BNF contributed 17.90 and 16.28% for these treatments respectively. Alfalfa has a higher BNF efficiency when grown in a mixture, initiating BNF earlier, and having higher N2 fixation due to less inhibition by soil-available N. For the greatest N-use-efficiency and sustainable production, grass-legume mixtures are recommended for improving grasslands, using a moderate amount of N fertilizer (75 kg N ha–1) to provide optimum benefits.
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Effect of Source-Sink Manipulation on Photosynthetic Characteristics of Flag Leaf and the Remobilization of Dry Mass and Nitrogen in Vegetative Organs of Wheat
ZHANG Ying-hua, SUN Na-na, HONG Jia-pei, ZHANG Qi, WANG Chao, XUE Qing-wu, ZHOU Shun-li, HUANG Qin , WANG Zhi-min
2014, 13 (8): 1680-1690.   DOI: 10.1016/S2095-3119(13)60665-6
Abstract1462)      PDF in ScienceDirect      
The photosynthetic characteristics of flag leaf and the accumulation and remobilization of pre-anthesis dry mass (DM) and nitrogen (N) in vegetable organs in nine wheat cultivars under different source-sink manipulation treatments including defoliation (DF), spike shading (SS) and half spikelets removal (SR) were investigated. Results showed that the SS treatment increased the photosynthetic rate (Pn) of flag leaf in source limited cultivar, but had no significant effect on sink limited cultivar. The SR treatment decreased the Pn of flag leaf. Grain DM accumulation was limited by source in some cultivars, in other cultivars, it was limited by sink. Grain N accumulation was mainly limited by source supply. The contribution of pre-anthesis dry mass to grain yield from high to low was stem, leaf and chaff, while the contribution of pre-anthesis N to grain N from high to low was leaf, stem and chaff. Cultivars S7221 and TA9818 can increase the contribution of remobilization of DM and N to grain at the maximum ratio under reducing source treatments, which may be the major reason for these cultivars having lower decrease in grain yield and N content under reducing source treatments.
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Effects of Dietary Energy Level on the Expression of the HSL Gene in Different Tissues of Sheep
ZHANG Ying-jie, LIU Yue-qin, CHENG Shan-yan, SONG Jie
2012, 12 (7): 1167-1172.   DOI: 10.1016/S1671-2927(00)8643
Abstract1197)      PDF in ScienceDirect      
A total of 36 four-mon-old hybrid lambs (Dorset×Thin-tailed Han sheep) with similar body weight (BW) were randomly allocated to three dietary treatments with different energy (7.21, 10.33 and 13.49 MJ d-1 ME) but similar protein levels. The animals were slaughtered and subcutaneous fat, longissimus dorsi muscle, femoral biceps muscle and cardiac muscle tissue samples were taken after being treated for 40 d. The samples were then subjected to quantitative PCR to determine mRNA expression of hormone-sensitive lipase (HSL) in different tissues in the laboratory. The findings showed that the abundance of HSL mRNA decreased with the elevation of dietary energy. In the subcutaneous fatty tissue, the HSL mRNA levels showed significant differences among the three groups (P<0.01); in the longissimus dorsi and femoral biceps muscles, the HSL mRNA level in the low energy group was significantly higher than that in the moderate and high energy groups (P<0.01). In the cardiac muscle, the HSL mRNA level in the moderate energy group was significantly different from the low and high energy groups (P<0.05). The number of HSL copies (Qty) in different tissues of sheep was different, it was greater in the subcutaneous fat than in longissimus dorsi muscle, femoral biceps muscle and heart.
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Effects of Papain Hydrolysis on the Pasting Properties of Wheat Flour
CHEN Jian-sheng, TIAN Ji-chun, DENG Zhi-ying, ZHANG Ying-xiang, FENG Shou-li, YAN Zuo-chen, ZHANG Xin-ye, YUAN Hui-qing
2012, 12 (12): 1948-1957.   DOI: 10.1016/S1671-2927(00)8731
Abstract1594)      PDF in ScienceDirect      
As one of the most effective enzymatic modification methods of protein, papain hydrolysis is applied widely in food production, accompanying starch pasting frequently in order to improve industrial quality. Effects of the papain hydrolysis on flour pasting properties were investigated in five papain/flour concentrations and five time-treatments. The structure of starch and protein networks in slurry was investigated under microscope before and after pasting. Results showed that papain hydrolysis influenced the pasting properties of wheat flour significantly through affecting structural characteristics, amylase activity and exothermic transition, especially during the early stage of hydrolysis. Peak viscosity, trough, final, integral area, and setback significantly decreased along with the increasing concentration of papain. Both hydrolysis time and concentration of papain had obviously effect on the breakdown. Pasting temperature and pasting time increased significantly with the enhancement of papain concentration. Hydrolysis time exerted minor effect on the pasting temperature and pasting time. The average peak time was slightly prolonged by lower concentration of papain, otherwise slightly shortened by higher concentration.
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