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Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F
2
chicken population
LI Yu-dong, BAI Xue, LIU Xin , WANG Wei-jia, LI Zi-wei, WANG Ning, XIAO Fan, GAO Hai-he, GUO Huai-shun, LI Hui, WANG Shou-zhi
2022, 21 (
7
): 2065-2075. DOI:
10.1016/S2095-3119(21)63805-4
Abstract
(
318
)
PDF in ScienceDirect
Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F
2
birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F
0
individuals were re-sequenced at a 10-fold depth; 519 F
2
individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (
F
ST
(fixation index) and θ
π
(nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW). A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb). A total of 17 positional candidate genes (PCGs) (
LRCH1
,
CDADC1
,
CAB39L
,
LOC112531568
,
LOC112531569
,
FAM124A
,
FOXO1
,
NBEA
,
GPALPP1
,
RUBCNL
,
ARL11
,
KPNA3
,
LHFP
,
GBA3
,
LOC112532426
,
KCNIP4
, and
SLIT2
) were identified in these regions. In particular,
KPNA3
and
FOXO1
were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.
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Identification and expression analysis of the
PbrMLO
gene family in pear, and functional verification of
PbrMLO23
GUO Bing-bing, LI Jia-ming, LIU Xing, QIAO Xin, Musana Rwalinda FABRICE, WANG Peng, ZHANG Shao-ling, WU Ju-you
2021, 20 (
9
): 2410-2423. DOI:
10.1016/S2095-3119(20)63558-4
Abstract
(
152
)
PDF in ScienceDirect
Mildew resistance locus O
(
MLO
) is a plant-specific gene family that plays an important role in the growth and development of plants and their interactions with the environment. However, the available information on this gene family in pear is limited. Here, 24
PbrMLO
genes were identified and divided into five subfamilies (I, II, III, IV and V). Whole-genome duplication (WGD) and dispersed duplication contributed to the expansion of the
PbrMLO
family. In addition, gene expression analysis revealed that
PbrMLO
genes were distributed in various pear tissues, suggesting their diverse functions. We selected
PbrMLO23
for further functional analysis. Expression profile analysis by qRT-PCR showed that
PbrMLO23
was highly expressed in pollen. Subcellular localization analysis showed that PbrMLO23 was located on the plasma membrane. When the expression level of
PbrMLO23
was knocked down by using antisense oligonucleotides, pollen tube lengths increased, indicating that
PbrMLO23
plays a functional role in inhibiting pollen tube growth. In summary, these results provide evolutionary insight into
PbrMLO
and its functional characteristics and lay a foundation for further analysis of the functions of
PbrMLO
members in pear.
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The effects of intraspecific competition and light transmission within the canopy on wheat yield in a wide-precision planting pattern
LIU Xin, WANG Wen-xin, LIN Xiang, GU Shu-bo, WANG Dong
2020, 19 (
6
): 1577-1585. DOI:
10.1016/S2095-3119(19)62724-3
Abstract
(
109
)
PDF in ScienceDirect
The wide-precision planting pattern has become widely used in the North China Plain as a practice for increasing wheat yield. However, the effects of tillering development and light transmission within canopy on wheat yield under different sowing widths have not been clearly described. Therefore, a two-year experiment was conducted, including four different seeding widths (6 cm, W6; 8 cm, W8; 10 cm, W10; 12 cm, W12) and the traditional planting pattern with seeding width of 4 cm (W4). The results indicated mainly positive effects by the reduced intraspecific competition, specifically all three yield components of W6 and W8 were higher than those for W4. The configurations with more than 10-cm seeding width were mainly affected by the negative effect of a relative homogeneous canopy, leading to the weakened light transmission, leaf senescence, and reduced grain number per spike. Finally, the yields of W6 and W8 were significantly higher than that of W4, whereas the yield in W12 was lower (though not significantly) than W4. In wheat production, therefore, the appropriate seeding width of 6–8 cm is recommended for farmers, whereas the too wide seeding width, with more than 10 cm, should be avoided.
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Comprehensive characterization of yam tuber nutrition and medicinal quality of
Dioscorea opposita
and
D. alata
from different geographic groups in China
SHAN Nan, WANG Pu-tao, ZHU Qiang-long, SUN Jing-yu, ZHANG Hong-yu, LIU Xing-yue, CAO Tian-xu, CHEN Xin, HUANG Ying-jin, ZHOU Qing-hong
2020, 19 (
11
): 2839-2848. DOI:
10.1016/S2095-3119(20)63270-1
Abstract
(
179
)
PDF in ScienceDirect
China is an important domestication center of yams, and two main yam species of
Dioscorea opposita
and
D. alata
are commonly cultivated in China. However, the differences of nutritional and medicinal characteristics between the two species and their subgroups remain unclear, which would greatly affect the resource conservation and commercial utilization of yams. In this study, typical yam resources including the species of
D. opposita
(wild and cultivated Ruichang yam from southern China, and Tiegun yam from northern China) and two landraces of
D. alata
(Longyan yam and Anyuan yam from southern China) were selected as materials. Nutritional traits and medicinal characteristics were determined and analyzed respectively. The results showed that there was no significant differences in the content of most nutrients between
D. opposita
and
D. alata
, but most cultivated Ruichang yam of
D. opposita
showed higher levels of starch, soluble sugar, sucrose, and ascorbate in tuber than that in yam from
D. alata
. Moreover, an UPLC-MS method was developed for identification and determination of medicinal characteristics in the two species. The results showed that allantoin can be detected in all selected samples. Cultivated Ruichang yam of
D. opposita
possessed the highest allantoin content among the tested materials, and was significantly different with that in Tiegun yam and
D. alata
. Dioscin was not detected in
D. alata
. Overall, there was little difference in nutritional composition between
D. opposita
and
D. alata
, but the medicinal quality of
D. opposita
was better than that of
D. alata
. Due to the outstanding comprehensive quality, the local variety of cultivated Ruichang yam can be further developed and utilized.
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Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (
Anas platyrhynchos
)
HUANG Yin-hua, FENG Hua-peng, HUANG Li-ren, YI Kang, RONG En-guang, CHEN Xiao-yun, LI Jian-wen, WANG Zeng, ZHU Peng-yang, LIU Xiao-juan, WANG Xiao-xue, HU Jia-xiang, LIU Xin, CHEN Hua-lan, WANG Jun...
2019, 18 (
7
): 1460-1472. DOI:
10.1016/S2095-3119(19)62646-8
Abstract
(
205
)
PDF in ScienceDirect
H5N1 influenza represents one of the great challenges to public health. Some H5N1 viruses (i.e., A/goose/Hubei/65/05, GS/65) are weakly pathogenic, while the others (i.e., A/duck/Hubei/49/05, DK/49) are highly pathogenic to their natural hosts. Here, we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus. We demonstrated that, compared to the GS/65 virus, the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways (i.e., RIG-I and MDA5) in ducks. We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes, while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus. We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis (WGCNA). Moreover, we first demonstrated that the duck
BCL2L15
and
DCSTAMP
in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently. These analyses, in combination with our comprehensive transcriptomic data, provided global view of the molecular architecture for the interaction between host and H5N1 viruses.
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Progress of the discovery, application, and control technologies of chemical pesticides in China
PAN Xing-lu, DONG Feng-shou, WU Xiao-hu, XU Jun, LIU Xin-gang, ZHENG Yong-quan
2019, 18 (
4
): 840-853. DOI:
10.1016/S2095-3119(18)61929-X
Abstract
(
281
)
PDF
(817KB)(
416
)
Pesticides, which have the dual characteristics of being both helpful and harmful, are important materials for ensuring food security and human health. Therefore, the rational development, scientific application, and effective control of pesticides are very important. In this paper, from the perspectives of pesticide discovery, formulation processing, application mode, residue monitoring, and pollution elimination and prediction, trends in the research progress and development of pesticides in China were systematically summarized to provide an important reference for the development of pesticides with high efficiency and low risk and for the reduction of pesticide application.
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Penicillium
and patulin distribution in pears contaminated with
Penicillium expansum
. Determination of patulin in pears by UHPLC-MS/MS
WEI Dong-mei, XU Jun, DONG Feng-shou, LIU Xin-gang, WU Xiao-hu, ZHENG Yong-quan
2017, 16 (
07
): 1645-1651. DOI:
10.1016/S2095-3119(16)61543-5
Abstract
(
1002
)
PDF in ScienceDirect
The danger of mycotoxin contamination entering the food supply through post-harvest infection is of perennial concern to food safety experts. To explore the distribution of
Penicillium expansum
and diffusion of its mycotoxin, patulin, in blue mold-damaged pears,
Pyrus bretschneideri
Rehd. cv.
Yali obtained
from markets and orchards in China were artificially inoculated with
P. expansum
and assayed for patulin accumulation and degree of fungal colonization. The inoculated pears were incubated until the lesions were 5, 10, 20, or 30 mm in diameter. We sampled tissue at a range of distances from the lesion, measured the spread of
Penicillium
by plate colony-counting methods, and used UHPLC-MS/MS to detect and quantify the patulin concentration. More
P. expansum
colony-forming units were isolated from pears with a higher degree of decay. Farther from the lesion, the fewer
P. expansum
colonies were observed, and the lower the patulin content detected. We found a significant difference in the patulin content between samples due to lesion size, and also in tissue sampled 10 mm away from the lesion. In consideration of this finding, to ensure food safety, we recommend that when a blue mold rot lesion on pear is 5, 10, or 20 mm in diameter, 20, 30, and 40 mm beyond the lesion should be removed, respectively. If a lesion surpasses 30 mm in diameter, the whole pear should be thrown away.
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Molecular cloning and functional characterization of
MdPIN1
in apple
AN Jian-ping, LIU Xin, LI Hao-hao, YOU Chun-xiang, SHU Jing, WANG Xiao-fei, HAO Yu-jin
2017, 16 (
05
): 1103-1111. DOI:
10.1016/S2095-3119(16)61554-X
Abstract
(
839
)
PDF in ScienceDirect
Auxin has been identified to play critical roles in regulating plant growth and development. The polar transport of auxin is regulated by auxin transporters. In the present study, an auxin efflux carrier gene
MdPIN1
was cloned from
Malus
×
domestic
, Royal Gala, and introduced into wild-type
Arabidopsis thaliana
(Col-0). The transgenic plants exhibited the phenotype of inhibition of primary root (PR) elongation and increased lateral root (LR) number in compared with Col-0. Overexpression of
MdPIN1
affected auxin transport, and enhanced phototropic responses and geotropism reaction, whereas had no significant difference in the auxin biosynthesis. These findings suggest that the
MdPIN1
gene plays a vital role in auxin transport and root development.
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Heritabilities and genetic and phenotypic correlations of litter uniformity and litter size in Large White sows
ZHANG Tian, WANG Li-gang, SHI Hui-bi, YAN Hua, ZHANG Long-chao, LIU Xin, PU Lei, LIANG Jing, ZHANG Yue-bo, ZHAO Ke-bin, WANG Li-xian
2016, 15 (
4
): 848-854. DOI:
10.1016/S2095-3119(15)61155-8
Abstract
(
2030
)
PDF in ScienceDirect
Litter uniformity, which is usually represented by within-litter weight coefficient of variation at birth (CVB), could influence litter performance of sows and the profitability of pig enterprises. The objective of this study was to characterize CVB and its effect on other reproductive traits in Large White sows. Genetic parameters and genetic correlation of the reproductive traits, including CVB, within-litter weight coefficient of variation at three weeks (CVT), total number born (TNB), number born alive (NBA), number born dead (NBD), gestation length (GL), piglet mortality at birth (M
0
), piglet mortality at three weeks (M
3
), total litter weight at birth (TLW0), and total litter weight at three weeks (TLW
3
) were estimated for 2 032 Large White litters. The effects of parity and classified litter size on CVB, CVT, TNB, NBA, NBD, GL, M
0
, M
3
, TLW
0
, and TLW
3
were also estimated. The heritabilities of these reproductive traits ranged from 0.06 to 0.17, with the lowest heritability for CVB and the highest heritability for TLW0. Phenotypic and genetic correlations between these reproductive traits were low to highly positive and negative (ranging from −0.03 to 0.93, and −0.53 to 0.93, respectively). The genetic correlations between TNB and CVB, and between M
0
and CVB were 0.32 and 0.29, respectively. In addition, CVB was significantly influenced by parity and litter size class (
P
<0.05). All the results suggest that piglet uniformity should be maintained in pig production practices and pig breeding programs.
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Influence of potato flour on dough rheological properties and quality of steamed bread
LIU Xing-li, MU Tai-hua, SUN Hong-nan, ZHANG Miao, CHEN Jing-wang
2016, 15 (
11
): 2666-2676. DOI:
10.1016/S2095-3119(16)61388-6
Abstract
(
2236
)
PDF in ScienceDirect
It is a novel idea to make steamed bread by adding potato flour into wheat flour considering the production and nutritional factors of potato. In this study, the influence of potato flour (0–35%) on dough rheology and quality of steamed bread were investigated. Potato flour addition significantly influenced the dough rheological properties and steamed bread quality, such as increased water absorption, the maximum gaseous release height, total volume of CO
2
and hardness, while decreased dough stability and specific volume of steamed bread. Moreover, correlation analysis suggested that dough height at the maximum development time, dough stability, water absorption and the phase tangent can be used for predicting the technological quality of steamed bread. Potato-wheat steamed bread had higher dietary fibre, ash content and antioxidant activity than those of wheat steamed bread. The estimated glycemic index decreased from 73.63 (0%) to 60.01 (35%). Considering the sensory evaluation, the steamed bread with 20% potato flour is acceptable. In conclusion, adding appropriate quantity of potato flour to wheat flour for steamed bread production will not only maintain the technological quality, but also can improve the nutritional value of the steamed bread.
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Porcine
LEM domain-containing 3
: Molecular cloning, functional characterization, and polymorphism associated with ear size
LIANG Jing, LI Na, ZHANG Long-chao, WANG Li-gang, LIU Xin, ZHAO Ke-bin, YAN Hua, PU Lei, ZHANG Yue-bo, SHI Hui-bi, ZHANG Qin, WANG Li-xian
2016, 15 (
06
): 1321-1229. DOI:
10.1016/S2095-3119(15)61173-X
Abstract
(
1356
)
PDF in ScienceDirect
Ear size exhibits remarkable diversity in pig breeds.
LEM domain-containing 3
(
LEMD3
) on chromosome 5 is considered as an important candidate for porcine ear size. This is the first study on cloning and characterization of
LEMD3
cDNA. The complete cDNA contains 4 843 bp, including a 2 736-bp open reading frame (ORF), a 37-bp 5´-untranslated region (UTR) and a 2 070-bp 3´-UTR. The complete LEMD3 gene is 126 241-bp and contains 13 exons and 12 introns. The ORF encodes a deduced LEMD3 protein of 911 amino acids, which shares 82–94% nucleic acid and 51–96% amino acid identity with other species. A phylogenetic tree constructed based on the amino acid sequences revealed that the porcine LEMD3 protein was closely related with cattle LEMD3. Resequencing of the ORF and promoter of
LEMD3
from Minzhu pig and Large White revealed three single nucleotide polymorphisms (SNPs): L964C>A in the complete coding region, L4625A>G in the 3´ UTR, and L-394T>C in the promoter region. Genome-wide association study (GWAS) revealed that all of SNPs were shown significant association with ear size in Large White×Minzhu pig intercross population. With conditional GWAS, –log
10
(
P
-value) decreased by more than 80% when each of three SNPs was included as a fixed effect. These results suggested direct involvement of
LEMD3
or close linkage to the causative mutation for ear size. The findings of this study might form the basis for understanding the genetic mechanism of ear size variation in pigs and provide potential molecular markers for screening ear size diversity in pig breeds.
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Investigation on the co-infections of Toxoplasma gondii with PRRSV, CSFV or PCV-2 in swine in part of China
Wang Shuai, ZHang Meng, LIU Xin-chao, LIn Tao, Yang Han-chun, YUan Shi-shan, ZHao guang-wei, Ia Hassan, Yan Ruo-feng, Song Xiao-kai, XU Li-xin, LI Xiang-rui
2015, 14 (
9
): 1838-1844. DOI:
10.1016/S2095-3119(15)61044-9
Abstract
(
1515
)
PDF in ScienceDirect
The objective of the present investigation was to estimate the prevalence of Toxoplasma gondii infection and co-infection with porcine reproductive and respiratory syndrome virus (PRRSV), classical swine fever virus (CSFV) and porcine circovirus type 2 (PCV-2) in pigs in China. A total of 372 tissues or serum samples collected from pigs distributed in 9 provinces/ municipalities of China during the period from February 2011 to November 2012 were assayed for T. gondii antigens and antibodies using enzyme linked immunosorbent assay (ELISA) technique, while the PCR was designed for the detection of the PRRSV, CSFV and PCV-2, respectively. The total positive rate of T. gondii, PRSSV, CSFV and PCV-2 was 9.14% (34/372), 50.00% (186/372), 37.10% (138/372) and 3.23% (12/372), respectively. Among the 34 T. gondii positive samples, 26 samples were simultaneously infected with T. gondii and viruses, while the remaining eight samples were infected with T. gondii alone. In addition, the co-infection rate of T. gondii with PRSSV, T. gondii with PRSSV and CSFV, T. gondii with PRSSV and PCV-2, T. gondii with CSFV and PCV-2, T. gondii with PRSSV, CSFV and PCV-2 was 1.61% (6/372), 4.03% (15/372), 0.27% (1/372), 0.27% (1/372) and 0.81% (3/372), respectively. The results of the present survey revealed that PRRSV and CSFV were the common pathogens co-existing with porcine toxoplasmosis in China, and both of them could increase the chances of T. gondii infection in pig. This is the first report of T. gondii co-infections with viruses in pigs. It is very important to understand the interactions of parasite and virus, and can be used as reference data for the control and prevention of co-infections of T. gondii and viruses in pigs.
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A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)
ZHAI Hui-jie, FENG Zhi-yu, LIU Xin-ye, CHENG Xue-jiao, PENG Hui-ru, YAO Ying-yin, SUN Qi-xin, NI Zhong-fu
2015, 14 (
9
): 1697-1705. DOI:
10.1016/S2095-3119(14)60902-3
Abstract
(
1693
)
PDF in ScienceDirect
The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.
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Interactions of water and nitrogen addition on soil microbial community composition and functional diversity depending on the inter-annual precipitation in a Chinese steppe
SUN Liang-jie, QI Yu-chun, DONG Yun-she, HE Ya-ting, PENG Qin, LIU Xin-chao, JIA Jun-qiang, GUO Shu-fang, CAO Cong-cong
2015, 14 (
4
): 788-799. DOI:
10.1016/S2095-3119(14)60773-5
Abstract
(
2021
)
PDF in ScienceDirect
Water and nitrogen are primary limiting factors in semiarid grassland ecosystems. Our knowledge is still poor regarding the interactive effects of water and N addition on soil microbial communities, although this information is crucial to reveal the mechanisms of the terrestrial ecosystem response to global changes. We addressed this problem by conducting a field experiment with a 15% surplus of the average rainfall under three levels of N addition (50, 100, and 200 kg N ha–1 yr–1) in two consecutive years in Inner Mongolia, China. Microbial community composition and functional diversity were analyzed based on phospholipid fatty acids (PLFA) and BIOLOG techniques, respectively. The results showed that water addition did not affect the soil microbial community composition, but much more yearly precipitation generally decreased the PLFA concentration, which implied a fast response of soil microbes to changes of water condition. Soil fungi was depressed only by N addition at the high level (200 kg N ha–1 yr–1) and without hydrologic leaching, while Gram-negative bacteria was suppressed probably by plant competition at high level N addition but with hydrologic leaching. The study found unilateral positive/negative interactions between water and N addition in affecting soil microbial community, however, climate condition (precipitation) could be a significant factor in disturbing the interactions. This study highlighted that: (1) The sustained effect of pulsed water addition was minimal on the soil microbial community composition but significant on the microbial community functional diversity and (2) the complex interaction between water and N addition on soil microbial community related to the inter-annual variation of the climate and plant response.
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Management of pesticide residues in China
CHEN Zeng-long, DONG Feng-shou, XU Jun, LIU Xin-gang, ZHENG Yong-quan
2015, 14 (
11
): 2319-2327. DOI:
10.1016/S2095-3119(15)61110-8
Abstract
(
1974
)
PDF in ScienceDirect
This paper reviewed management of pesticide residues in China including laws and regulations, the supervision system, the standard system, and the quality and safety of agricultural products. The process of establishment and internationalization of standards for pesticide residues were also discussed. Results indicate that the progress of the management of pesticide residues has been steadily made in China. However, the following aspects which refer to updates to regulations, supervising efficiency, standard system, risk assessment, international cooperation and communication, should be further improved. China should draw lessons from international experience, and then establish its own management system, which focuses on pesticides controls by strictly following relevant laws and technical standards to ensure the quality and safety of agricultural products.
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Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs
ZHANG Long-chao, LIU Xin, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, PU Lei, SHI Hui-bi, ZHANG Yue-bo, WANG Li-gang, WANG Li-xian
2015, 14 (
10
): 2027-2033. DOI:
10.1016/S2095-3119(15)61084-X
Abstract
(
1646
)
PDF in ScienceDirect
Although quantitative trait loci (QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes (SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait (number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60K chip. Performing a genome-wide association study (GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor (NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin (VRTN), prospero homeobox 2 (PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog (FOS), and transforming growth factor beta 3 (TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.
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Impact of fluxapyroxad on the microbial community structure and functional diversity in the silty-loam soil
WU Xiao-hu, XU Jun, LIU Yong-zhuo, DONG Feng-shou, LIU Xin-gang, ZHANG Wen-wen, ZHENG Yong-quan
2015, 14 (
1
): 114-124. DOI:
10.1016/S2095-3119(14)60746-2
Abstract
(
1842
)
PDF in ScienceDirect
The aim of this work was to assess the effect of applying three different doses of fluxapyroxad on microbial activity, community structure and functional diversity as measured by respiration, microbial biomass C, phospholipid fatty acid (PLFA) and community-level physiological profiles (CLPPs). Our results demonstrated that substrate-induced respiration (on day 15) and microbial biomass C (on days 7 and 15) were inhibited by fluxapyroxad, but stimulation was observed thereafter. In contrast, fluxapyroxad addition increased the basal respiration and metabolic quotients (qCO2) and respiratory quotients (QR). Analysis of the PLFA profiles revealed that the total and bacterial biomass (both Gram-positive bacteria (GP) and Gram-negative bacteria (GN)) were decreased within the initial 15 days, whereas those as well as the GN/GP ratio were increased at days 30 and 60. Fluxapyroxad input decreased the fungi biomass but increased the bacteria/fungi ratio at all incubation time. Moreover, high fluxapyroxad input (75 mg fluxapyroxad kg–1 soil dry weight) increased the microbial stress level. A principal component analysis (PCA) of the PLFAs revealed that fluxapyroxad treatment significantly shifted the microbial community structure, but all of the observed effects were transient. Biolog results showed that average well color development (AWCD) and functional diversity index (H´) were increased only on day 60. In addition, the dissipation of fluxapyroxad was slow in soil, and the degradation half-lives varied from 158 to 385 days depending on the concentration tested.
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Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population
LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian
2014, 13 (
12
): 2721-2730. DOI:
10.1016/S2095-3119(14)60787-5
Abstract
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1694
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Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.
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Dissipation and Adsorption Behavior of the Insecticide Ethiprole on Various Cultivated Soils in China
LIU Xin-gang, DONG Feng-shou, XU Jun, YUAN Shan-kui , ZHENG Yong-quan
2014, 13 (
11
): 2471-2478. DOI:
10.1016/S2095-3119(13)60685-1
Abstract
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1087
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In this study, the hydrolysis of the insecticide ethiprole in buffered solutions at pH 4.0, 7.0 and 9.0, respectively, and the degradation and adsorption-desorption behaviors of ethiprole in five agricultural soil samples from China were investigated. The half-lives under anaerobic conditions were faster than that in the aerobic experiment. Ethiprole was relatively stable under both acidic and neutral conditions while it was readily hydrolyzed under alkaling condition. The sorption of ethiprole on five soils was well described by the linear and Freundlich equation and mainly governed by soil organic matter. The exothermic process of ethiprole adsorption can also be well explained by physical adsorption. A weak adsorption capacity was observed in all soils, which could readily lead to leaching problems.
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Maize Yield Gains in Northeast China in the Last Six Decades
NIU Xing-kui, XIE Rui-zhi, LIU Xin, ZHANG Feng-lu, LI Shao-kun , GAO Shi-ju
2013, 12 (
4
): 630-637. DOI:
10.1016/S2095-3119(13)60281-6
Abstract
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1710
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In 2010, Chinese maize yields increased from 961.5 kg ha-1 in 1949 to 5 453.8 kg ha-1. This increase is the result of genetic improvements, an increase in nitrogen application, and refinement of planting densities. The objective of this study was to provide a theoretical basis for maize production research by analyzing the maize yield gain characteristics. Six varieties of maize were selected for the study; each selection is representative of a typical or commonly used maize variety from a specific decade, beginning from the 1950s and continuing through each decade into the 2000s. The selections and their corresponding decade were as follows: Baihe, 1950s; Jidan 101, 1960s; Zhongdan 2, 1970s; Yedan 13, 1980s; Zhengdan 958, 1990s; and Xianyu 335, 2000s. Each variety was planted under four different densities (37 500, 52 500, 67 500, and 82 500 plants ha-1) and four different nitrogen applications (0, 150, 225, and 300 kg ha-1) to study the effects on yield gain characteristics. The obtained results demonstrated that there was a maize yield increase of 123.19% between the 1950s variety and the 2000s variety. Modern Chinese maize varieties had a higher yield advantage. They also displayed the additional potential to acquire higher yield under increased planting densities and nitrogen applications. At the present cultivation levels (planting at 67 500 plants ha-1 with 225 kg ha-1 nitrogen application), the contribution types and corresponding yield increase percentages were as follows: genetic improvement, 45.37%; agronomic-management improvement, 30.94%; and genotype× agronomicmanagement interaction, 23.69%. At high-yielding cultivation levels (planting at 82 500 plants ha-1 with 300 kg ha-1 nitrogen application), the contribution types and corresponding yield increase percentages were as follows: genetic improvement, 31.30%; agronomic-management improvement, 36.23%; and genotype × agronomic-management interaction, 32.47%. The contribution of agronomic-management and genotype × agronomic-management interaction to yield increase would be larger with the corresponding management improvement. To further increase maize grain yield in China, researchers should further examine the effects of agronomic-management on maize yield and the adaptation of variety to agronomic-management.
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Assessing Maize Drought Hazard for Agricultural Areas Based on the Fuzzy Gamma Model
LIU Xing-peng, ZHANG Ji-quan, CAI Wei-ying , TONG Zhi-jun
2013, 12 (
3
): 532-540. DOI:
10.1016/S2095-3119(13)60254-3
Abstract
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1424
)
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Drought is one of the severe meteorological disasters and causes of serious losses for agricultural productions, and early assessment of drought hazard degree is critical in management of maize farming. This study proposes a novel method for assessment of maize drought hazard in different growth stages. First, the study divided the maize growth period into four critical growth stages, including seeding, elongation, tasseling, and filling. Second, maize drought causal factors were selected and the fuzzy membership function was established. Finally, the study built a fuzzy gamma model to assess maize drought hazards, and the gamma 0.93 was finally established using Monte Carlo Analysis. Performing fuzzy gamma operation with 0.93 for gamma and classifying the area yielded a map of maize drought hazards with four zones of light, moderate, severe, and extreme droughts. Using actual field collected data, seven selected samples for drought hazard degree were examined, the model output proved to be a valid tool in the assessment maize drought hazard. This model will be very useful in analyzing the spatial change of maize drought hazard and influence on yield, which is significant for drought management in major agricultural areas.
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Studies on the Root Characteristics of Maize Varieties of Different Eras
ZHANG Feng-lu, NIU Xing-kui, ZHANG Yi-ming, XIE Rui-zhi, LIU Xin, LI Shao-kun , GAO Shi-ju
2013, 12 (
3
): 426-435. DOI:
10.1016/S2095-3119(13)60243-9
Abstract
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1419
)
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Experiment was conducted at the Gongzhuling Experimental Station of Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Jilin Province, China, during 2009-2010. Six representative varieties of maize (Baihe in the 1950s, Jidan 101 in the 1960s, Zhongdan 2 in the 1970s, Yedan 13 in the 1980s, Zhengdan 958 in the 1990s, and Xianyu 335 in the 2000s) were each planted under two different densities (52 500 and 82 500 plants ha-1) and two different nitrogen application levels (150 and 300 kg ha-1). Root characteristics and distribution among soil layers were studied by the field root digging method. The results showed that root mass increased with the process of the growth and development of the plant, and it peaked at kernel filling stage, and decreased at maturity due to the root senesces. Root mass of different maize varieties from the 1950s to 1980s had a trend of increase, while it decreased for the modern varieties. Root length and root surface areas had the similar changing trend. The study suggested that early maize varieties may have root redundancy, and reducing root redundancy may be a direction for variety improvement for high yield. Root characteristics were affected by nitrogen application level and density; modern varieties were more suitable for higher fertilizer application level and density conditions. Root characteristics distribution among soil layers decreased by an exponent equation, but the regression coefficients of different varieties were different. Though the root length density (RLD) of every soil layer of different varieties also decreased by an exponent equation, there were large variations of RLD in every part of a layer.
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Pathogenesis of Demyelinating Encephalopathy in Dogs with Spontaneous Acute Canine Distemper
PAN Yao-qian, LIU Xing-you, MENG Li-ping, ZHU Guang-rui, XIA Yin-ke, CHEN Jin-shan , Yoshikawa Takashi
2013, 12 (
2
): 334-343. DOI:
10.1016/S2095-3119(13)60233-6
Abstract
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1577
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So far, the pathogenesis of demyelination caused by canine distemper virus (CDV) in the central nervous system has remained unclear, although a lot of studies have been done extensively. To further investigate the relation of variety cells in brain to demyelination, this study was performed on 15 dogs with spontaneous acute canine distemper and 2 controls. According to anatomical relation, the brain was divided into cerebrum, cerebral stem and cerebellum. The sections with no, mild, moderate, or severe demyelinating lesions were selected respectively and stained by HE and immunohistochemistry. Immuno-localisation of CDV antigen was used to confirm CDV infection. The brain was examined for co-localisation of the CDV antigen with either an astrocyte-specific marker, glial fibrillary acidic protein (GFAP), or an oligodendrocyte-specific marker, galactocerebroside (GalC). Apoptotic cell was detected by TdT-mediated nick end-labeling assay (TUNEL). The results demonstrated that the local disturbance of blood circulation mainly included congestion, edema, thrombosis, and disseminated intravascular coagulation (DIC). The CDV neucleocapsid protein positive reaction, metabolic disorder and apoptosis of oligodendrocytes were observed in demyelinating areas. Lots of astrocytes displayed CDV antigen-positive, especially in their process. Some of them became apoptotic cell confirmed by TUNEL staining. Fibrous astrocytes showed more intense GFAP-positive in mild and moderate demyelinating area. Some of nervous cells located in pyramidal cell layers and nucleus nervi were in degeneration, necrosis. Satellitosis, neuronophagia and apoptotic neurons were examined by hematoxylin and eosin (HE) and TUNEL staining. The results suggested that the demyelinating changes in brain tissues infected with CDV mainly related to the metabolic disorder and apoptosis of ogliodendrocytes and astrocytes; also involved with the local disturbance of blood circulation and some neuron lost.
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Regulatory Function of Polyamine Oxidase-Generated Hydrogen Peroxide in Ethylene-Induced Stomatal Closure in Arabidopsis thaliana
HOU Zhi-hui, LIU Guo-hua, HOU Li-xia, WANG Lan-xiang , LIU Xin
2013, 12 (
2
): 251-262. DOI:
10.1016/S2095-3119(13)60224-5
Abstract
(
1746
)
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Hydrogen peroxide (H2O2) is an important signaling molecule in ethylene-induced stomatal closure in Arabidopsis thaliana. Early studies on the sources of H2O2 mainly focused on NADPH oxidases and cell-wall peroxidases. Here, we report the involvement of polyamine oxidases (PAOs) in ethylene-induced H2O2 production in guard cells. In Arabidopsis epidermal peels, application of PAO inhibitors caused the failure of ethylene to induce H2O2 production and stomatal closure. Results of quantitative RT-PCR analysis and pharmacological experiments showed that AtPAO2 and AtPAO4 transcripts and activities of PAOs were both induced by ethylene. In transgenic Arabidopsis plants over-expressing AtPAO2 and AtPAO4, stomatal movement was more sensitive to ethylene treatment and H2O2 production was also significantly induced. The increased H2O2 production in the transgenic lines compared to the wild-type plants suggests that AtPAO2 and AtPAO4 probably are involved in ethylene-induced H2O2 production. Several factors which induce stomatal closure such as dehydration and high salinity all enhanced the expression of AtPAO2 and AtPAO4 to different degrees. Moreover, GFPAtPAOs fusion protein localized in the nucleus, cytoplasm, and cell wall of the guard cells. Therefore, our results strongly indicated that PAO is a source of H2O2 generation in Arabidopsis guard cells and plays crucial roles in stomatal movement.
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ASimpleMethod for the Isolation andPurification of 2,4-Dihydroxy-7-Methoxy- 2H-1,4-Benzoxazin-3(4H)-One (DIMBOA) from Maize (Zea mays L.) Seedlings
LI Jing, LIU Xin-gang, DONG Feng-shou, XU Jun, GUO Li-qun, KONG Zhi-qiang, TIAN Ying-ying, WU Yan-bin , ZHENG Yong-quan
2013, 12 (
1
): 95-102. DOI:
10.1016/S2095-3119(13)60209-9
Abstract
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1590
)
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2,4-Dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), the dominant benzoxazinoid hydroxamic acid in maize (Zea Mays L.), serves as important factors of resistance against insects and microbial diseases, allelochemicals used in competition with other plants. In this paper, a novel and simple method for the isolation and purification of DIMBOA from maize seedlings was developed. Frozen shoots from 7-d-old maize seedlings (1 000×g) were firstly defrosted and then were directly homogenized and extracted with ethyl acetate. The macerate was allowed to stand at room temperature (25±2)°C for 1 h to allow enzymatic release of DIMBOA from DIMBOA-glucoside. Then the ethyl acetate phase was filtered, dried and evaporated to dryness. The resulting light-tan, semicrystalline residue was stored at -20°C for 24 h. Upon recrystallization from acetone-hexane, a relative higher yield (0.58 g) of pure DIMBOA crystals was obtained compared with the yield afforded by Woodward methodology (0.26 g).
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Hydrogen Sulfide May Function Downstream of Nitric Oxide in Ethylene- Induced Stomatal Closure in Vicia faba L.
LIU Jing, HOU Zhi-hui, LIU Guo-hua, HOU Li-xia, LIU Xin
2012, 12 (
10
): 1644-1653. DOI:
10.1016/S1671-2927(00)8697
Abstract
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1354
)
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Pharmacological, laser scanning confocal microscopic (LSCM), and spectrophotographic approaches were used to study the roles of hydrogen sulfide (H2S) and nitric oxide (NO) in signaling transduction of stomatal movement in response to ethylene in Vicia faba L. Ethylene treatment resulted in the dose-dependent stomatal closure under light, and this effect was blocked by the inhibitors of H2S biosynthesis in V. faba L. Additionally, ethylene induces H2S generation and increases L-/D-cysteine desulfhydrase (pyridoxalphosphate-dependent enzyme) activity in leaves of V. faba L. Inhibitors of H2S biosynthesis have no effect on the ethylene-induced stomatal closure, NO accumulation, and nitrate reductase (NR) activity in guard cells or leaves of V. faba L. Moreover, the ethylene-induced increase of H2S levels and L-/Dcysteine desulfhydrase activity declined when NO generation was inhibited. Therefore, we conclude that H2S and NO probably are involved in the signal transduction pathway of ethylene-induced stomatal closure. H2S may represent a novel component downstream of NO in the ethylene-induced stomatal movement in V. faba L.
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