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Dissecting the genetic basis of grain color and pre-harvest sprouting resistance in common wheat by association analysis

YAN Sheng-nan, YU Zhao-yu, GAO Wei, WANG Xu-yang, CAO Jia-jia, LU Jie, MA Chuan-xi, CHANG Cheng, ZHANG Hai-ping

2023, 22 (9): 2617-2631. DOI: 10.1016/j.jia.2023.04.017

Abstract （262） PDF in ScienceDirect

Pre-harvest sprouting (PHS) adversely affects wheat quality and yield, and grain color (GC) is associated with PHS resistance. However, the genetic relationship between GC and PHS resistance remains unclear. In this study, 168 wheat varieties (lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array. Genome-wide association study (GWAS) based on a mixed linear model showed that 67 marker-trait associations (MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation. In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation. Subsequently, two cleaved amplified polymorphic sequences (CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B, were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4 controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively. Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments (P<0.05). Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4. The new CAPS marker CAPS-356 was then developed based on the SNP (T/C) in the coding sequences (CDS) region of TraesCS5B02G545100. The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines (RILs) constructed based on speciﬁc locus ampliﬁed fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4. These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.

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Soil conditioners improve Cd-contaminated farmland soil microbial communities to inhibit Cd accumulation in rice

ZHAO Jun-yang, LU Hua-ming, QIN Shu-tao, PAN Peng, TANG Shi-de, CHEN Li-hong, WANG Xue-li, TANG Fang-yu, TAN Zheng-long, WEN Rong-hui, HE Bing

2023, 22 (8): 2521-2535. DOI: 10.1016/j.jia.2023.02.023

Abstract （208） PDF in ScienceDirect

The addition of silicon (Si) and organic fertilizers to soil conditioners can inhibit the transfer of heavy metal ions from soil to crops. However, it is not clear how Si and organic fertilizers affect soil properties and the micro-ecological environment and thereby reduce cadmium (Cd) accumulation in rice. In this study, the effects of L-type soil conditioners containing Si and organic fertilizers on bacterial and fungal community diversity, soil pH, organic matter, and available Si were analyzed with field experiments at two sites in Liuzhou City and Hezhou City, respectively, in Guangxi, China. With the increase of Si and organic fertilizer content in soil conditioner, rice yield respectively increased by 16.8–25.8 and 6.8–13.1%, and rice Cd content decreased significantly by 8.2–21.1 and 10.8–40.6%, respectively, at the two experimental sites. Soil microbiome analysis showed that the increase in abundance of Firmicutes and Actinobacteriota bacteria associated with Cd adsorption and sequestration, and Basidiomycota fungal populations associated with degradation of macromolecules favored the inhibition of soil Cd activity (soil exchangeable Cd decreased by 14.4–14.8 and 18.1–20.6%). This was associated with an increase in organic matter and Si content caused by applying soil conditioners. In conclusion, L-type soil conditioners, rich in Si and organic fertilizer, can reduce soil Cd bioavailability by regulating the dominant Cd passivating flora in the soil and ultimately reduce Cd accumulation in rice.

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A 2-bp frameshift deletion at GhDR, which encodes a B-BOX protein that co-segregates with the dwarf-red phenotype in Gossypium hirsutum L.

WANG Xue-feng, SHAO Dong-nan, LIANG Qian, FENG Xiao-kang, ZHU Qian-hao, YANG Yong-lin, LIU Feng, ZHANG Xin-yu, LI Yan-jun, SUN Jie, XUE Fei

2023, 22 (7): 2000-2014. DOI: 10.1016/j.jia.2022.10.007

Abstract （291） PDF in ScienceDirect

Plant architecture and leaf color are important factors influencing cotton fiber yield. In this study, based on genetic analysis, stem paraffin sectioning, and phytohormone treatments, we showed that the dwarf-red (DR) cotton mutant is a gibberellin-sensitive mutant caused by a mutation in a single dominant locus, designated GhDR. Using bulked segregant analysis (BSA) and genotyping by target sequencing (GBTS) approaches, we located the causative mutation to a ~197-kb genetic interval on chromosome A09 containing 25 annotated genes. Based on gene annotation and expression changes between the mutant and normal plants, GH_A09G2280 was considered to be the best candidate gene responsible for the dwarf and red mutant phenotypes. A 2-nucleotide deletion was found in the coding region of GhDR/GH_A09G2280 in the DR mutant, which caused a frameshift and truncation of GhDR. GhDR is a homolog of Arabidopsis AtBBX24, and encodes a B-box zinc finger protein. The frameshift deletion eliminated the C-terminal nuclear localization domain and the VP domain of GhDR, and altered its subcellular localization. A comparative transcriptome analysis demonstrated downregulation of the key genes involved in gibberellin biosynthesis and the signaling transduction network, as well as upregulation of the genes related to gibberellin degradation and the anthocyanin biosynthetic pathway in the DR mutant. The results of this study revealed the potential molecular basis by which plant architecture and anthocyanin accumulation are regulated in cotton.

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Development and pathogenicity analysis of full-length infectious cDNA clones of citrus yellow mottle-associated virus in citrus plants

WU Jia-xing, ZHANG Song, LIANG Xiao-fei, XING Fei, Sagheer ATTA, WANG Xue-feng, CAO Meng-ji

2023, 22 (10): 3034-3041. DOI: 10.1016/j.jia.2023.08.014

Abstract （187） PDF in ScienceDirect

Citrus yellow mottle-associated virus (CiYMaV) belonging to the subgenus Mandarivirus within the genus Potexvirus, was first identified in 2018 from Pakistan (CiYMaV-PK), where it is endemic in several regions. Here, three full-length cDNA clones (pCiYMaV-FL-1, pCiYMaV-FL-18, and pCiYMaV-FL-22) corresponding to the genomic RNA of CiYMaV were constructed and then agroinfiltrated on Chandler pummelo (Citrus grandis) seedlings using the vacuum infiltration method. All the inoculated plants developed severe vein yellowing, leaf mottling, and dwarfing symptoms by 40 days post-infiltration (dpi). The results of a direct tissue blot immunoassay and reverse transcription polymerase chain reaction detection showed 94.7–100% infection rates of pCiYMaV-FL at 60 dpi. Despite there being no observed difference among the three clones in the severity of symptom, pCiYMaV-FL-22 showed the highest accumulation levels of viral RNA and coat proteins. Moreover, pCiYMaV-FL-22 successfully infected seven other citrus varieties and induced symptoms in five of them. Transmission electron microscopy identified the presence of filamentous virus particles in extracts from systemic leaves of the plants infected with pCiYMaV-FL-22 at 6-months post-infiltration. Taken together, the results indicate that Koch’s postulates were fulfilled for CiYMaV in citrus plants. This is the first report of full-length infectious cDNA clones of CiYMaV, and thus, the data provide a basis for further study of the molecular mechanisms of virus infection and the development of a viral vector to express foreign genes in citrus plants.

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Transcriptomic analysis elucidates the enhanced skeletal muscle mass, reduced fat accumulation, and metabolically benign liver in human follistatin-344 transgenic pigs

LONG Ke-ren, LI Xiao-kai, ZHANG Ruo-wei, GU Yi-ren, DU Min-jie, XING Xiang-yang, DU Jia-xiang, MAI Miao-miao, WANG Jing, JIN Long, TANG Qian-zi, HU Si-lu, MA Ji-deng, WANG Xun, PAN Deng-ke, LI Ming-zhou

2022, 21 (9): 2675-2690. DOI: 10.1016/j.jia.2022.07.014

Abstract （325） PDF in ScienceDirect

Follistatin (FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β (TGF-β) superfamily, and thus may be a good candidate for future animal breeding programs. However, the molecular mechanisms underlying the phenotypic changes have yet to be clarified in pig. We generated transgenic (TG) pigs that express human FST specifically in skeletal muscle tissues and characterized the phenotypic changes compared with the same tissues in wild-type pigs. The TG pigs showed increased skeletal muscle growth, decreased adipose deposition, and improved metabolism status (P<0.05). Transcriptome analysis detected important roles of the PIK3–AKT signaling pathway, calcium-mediated signaling pathway, and amino acid metabolism pathway in FST-induced skeletal muscle hypertrophy, and depot-specific oxidative metabolism changes in psoas major muscle. Furthermore, the lipid metabolism-related process was changed in adipose tissue in the TG pigs. Gene set enrichment analysis revealed that genes related to lipid synthesis, lipid catabolism, and lipid storage were down-regulated (P<0.01) in the TG pigs for subcutaneous fat, whereas genes related to lipid catabolism were significantly up-regulated (P<0.05) in the TG pigs for retroperitoneal fat compared with their expression levels in wild-type pigs. In liver, genes related to the TGF-β signaling pathway were over-represented in the TG pigs, which is consistent with the inhibitory role of FST in regulating TGF-β signaling. Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.

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A rapid multiplication system for 'Candidatus Liberibacter asiaticus' through regeneration of axillary buds in vitro

LEI Tian-gang, HE Yong-rui, ZOU Xiu-ping, WANG Xue-feng, FU Shi-min, PENG Ai-hong, XU Lan-zhen, YAO Li-xiao, CHEN Shan-chun, ZHOU Chang-yong

2022, 21 (6): 1683-1693. DOI: 10.1016/S2095-3119(21)63856-X

Abstract （198） PDF in ScienceDirect

‘Candidatus Liberibacter asiaticus (CLas)’, which causes citrus Huanglongbing (HLB) disease, has not been successfully cultured in vitro to date. Here, a rapid multiplication system for CLas was established through in vitro regeneration of axillary buds from CLas-infected ‘Changyecheng’ sweet orange (Citrus sinensis Osbeck). Firstly, stem segments with a single axillary bud were cultured in vitro to allow CLas to multiply in the regenerating axillary buds. A high CLas titer was detected in the regenerated shoots on an optimized medium at 30 days after germination (DAG), and it was 28.2-fold higher than in the midribs from CLas-infected trees growing in the greenhouse. To minimize contamination during in vitro regeneration, CLas-infected axillary buds were micrografted onto seedlings of ‘Changyecheng’ sweet orange and cultured in a liquid medium. In this culture, the titers of CLas in regenerated shoots rapidly increased from 7.5×10⁴ to 1.4×10⁸ cells μg^-1 of citrus DNA during the first 40 DAG. The percentages of shoots with >1×10⁸ CLas cells μg^-1 DNA were 30% and 40% at 30 and 40 DAG, respectively. Direct tissue blot immune assay (DTBIA) indicated that the distribution of CLas was much more uniform in regenerated plantlets than in CLas-infected trees growing in the greenhouse. The disease symptoms in the plantlets were die-back, stunted growth, leaf necrosis/yellowing, and defoliation. The death rate of the plantlets was 82.0% at 60 DAG. Our results show that CLas can effectively multiply in in vitro culture. This method will be useful for studying plant–HLB interactions and for rapid screening of therapeutic compounds against CLas in citrus.

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Detection of antimicrobial resistance and virulence-related genes in Streptococcus uberis and Streptococcus parauberis isolated from clinical bovine mastitis cases in northwestern China

ZHANG Hang, YANG Feng, LI Xin-pu, LUO Jin-yin, WANG Ling, ZHOU Yu-long, YAN Yong, WANG Xu-rong, LI Hong-sheng

2020, 19 (11): 2784-2791. DOI: 10.1016/S2095-3119(20)63185-9

Abstract （118） PDF in ScienceDirect

The objectives of this study were to investigate antimicrobial resistance of Streptococcus uberis and Streptococcus parauberis isolated from cows with bovine clinical mastitis in China and to examine the distribution of resistance- and virulence-related gene patterns. Antimicrobial susceptibility was determined by the E-test. Genes encoding antimicrobial resistance and invasiveness factors were examined by PCR. A total of 27 strains were obtained from 326 mastitis milk samples. Streptococcus parauberis isolates (n=11) showed high resistance to erythromycin (90.9%), followed by tetracycline (45.5%), chloramphenicol (36.4%) and clindamycin (27.3%). Streptococcus uberis isolates (n=16) were highly resistant to tetracycline (81.3%) and clindamycin (62.5%). Both species were susceptible to ampicillin. The most prevalent resistance gene in S. uberis was tetM (80.0%), followed by blaZ (62.5%) and ermB (62.5%). However, tetM, blaZ, and ermB genes were only found in 27.3, 45.5, and 27.3%, respectively, of S. parauberis. In addition, all of the isolates carried at least one selected virulence-related gene. The most prevalent virulence-associated gene pattern in the current study was sua+pauA/skc+gapC+hasC detected in 22.2% of the strains. One S. uberis strain carried 7 virulence-associated genes and belonged to the sua+pauA/skc+gapC+cfu+hasA+hasB+hasC pattern. More than 59.3% of analysed strains carried 4 to 7 virulence-related genes. Our findings demonstrated that S. parauberis and S. uberis isolated from clinical bovine mastitis cases in China exhibited diverse molecular ecology, and that the strains were highly resistant to antibiotics commonly used in the dairy cow industry. The data obtained in the current study contribute to a better understanding of the pathogenesis of bacteria in mastitis caused by these pathogens, and the findings are relevant to the development of multivalent vaccines and targeted prevention procedures.

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Decreasing detection frequency of MITE (MCLas-A) in the population of ‘Candidatus Liberibacter asiaticus’ recently collected in southern China

CUI Xue-jin, ZENG Chun-hua, LIU Ke-hong, TENG Cai-ling, ZHOU Chang-yong, WANG Xue-feng

2020, 19 (10): 2597-2601. DOI: 10.1016/S2095-3119(20)63217-8

Abstract （119） PDF in ScienceDirect

An active miniature inverted-repeat transposable element (MITE), MCLas-A, was previously identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease). To explore the recent transposition status of MCLas-A, 389 ‘Ca. L. asiaticus’ strains collected from nine regions in China were amplified using a specific primer set and three representative ‘Ca. L. asiaticus’ strains were analyzed by next-generation sequencing (NGS) approach. PCR and genomic analysis showed that the entire MCLas-A was only present in 1.80% (7/389) and the jumping-out type of the MITE was predominant (81.23%) in samples tested, suggesting high frequency transposition occurred in ‘Ca. L. asiaticus’ strains recently collected from China. Biological roles of transposition of the active MITE remain to be determined.

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Internal phosphate starvation signaling and external phosphate availability have no obvious effect on the accumulation of cadmium in rice

WANG Xue-qing, RUAN Wen-yuan, YI Ke-ke

2019, 18 (9): 2153-2161. DOI: 10.1016/S2095-3119(18)62100-8

Abstract （121） PDF in ScienceDirect

Phosphorus (P) is a limiting nutrient element for crop. To obtain maximum crop yield, P fertilizer is often over-applied, which leads to accelerating exhaustion of phosphate resources and serious environmental problems. Reducing the application of P fertilizer and enhancing the P utilization efficiency of crops are significant for the sustainable development of agriculture. Cadmium (Cd) contamination in rice is another serious agricultural issue. However, whether reducing the application of P fertilizer and enhancing the P utilization efficiency of crops will increase the risk of Cd accumulation in crops remains obscure. In this study, we are aiming to elucidate the relationship between Cd and P in rice from physiological and genetic perspectives. For this purpose, the wild type (WT) rice plants and phosphate (Pi)-starvation signaling repressed mutant phr2 were used to analyze the relationship between Cd and P. Here, we found that Cd stress could promote P accumulation and induce Pi-starvation signaling in WT and phr2 shoots under Pi-sufficient condition in a PHOSPHATE STARVATION RESPONSE 2 (PHR2) independent manner. Besides, the expression level of Cd transporter of OsNramp5 and the uptake speed of Cd²⁺ were not obviously changed under Pi-sufficient and Pi-deficient conditions. Furthermore, our Cd determination results showed that the Cd concentrations in WT and phr2 were not obviously changed under Pi-sufficient and Pi-deficient conditions. These results indicate that the external P availability and internal Pi-starvation signaling cannot obviously affect the accumulation of Cd in rice seedling.

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Effects of planting patterns on yield, quality, and defoliation in machine-harvested cotton

WANG Fang-yong, HAN Huan-yong, LIN Hai, CHEN Bing, KONG Xian-hui, NING Xin-zhu, WANG Xu-wen, YU Yu, LIU Jing-de

2019, 18 (9): 2019-2028. DOI: 10.1016/S2095-3119(19)62604-3

Abstract （122） PDF in ScienceDirect

The aim of this study was to elucidate the effects of different machine-harvested cotton-planting patterns on defoliation, yield, and fiber quality in cotton and to provide support for improving the quality of machine-harvested cotton. In the 2015 and 2016 growing seasons, the Xinluzao 45 (XLZ45) and Xinluzao 62 (XLZ62) cultivars, which are primarily cultivated in northern Xinjiang, were used as study materials. Conventional wide-narrow row (WNR), wide and ultra-narrow row (UNR), wide-row spacing with high density (HWR), and wide-row spacing with low density (LWR) planting patterns were used to assess the effects of planting patterns on defoliation, yield, and fiber quality. Compared with WNR, the seed cotton yields were significantly decreased by 2.06–5.48% for UNR and by 2.50–6.99% for LWR, respectively. The main cause of reduced yield was a reduction in bolls per unit area. The variation in HWR yield was –1.07–1.07% with reduced bolls per unit area and increased boll weight, thus demonstrating stable production. In terms of fiber quality indicators, the planting patterns only showed significant effects on the micronaire value, with wide-row spacing patterns showing an increase in the micronaire values. The defoliation and boll-opening results showed that the number of leaves and dried leaves in HWR was the lowest among the four planting patterns. Prior to the application of defoliating agent and before machine-harvesting, the numbers of leaves per individual plant in HWR were decreased by 14.45 and 25.00% on average, respectively, compared with WNR, while the number of leaves per unit area was decreased by 27.44 and 36.21% on average, respectively. The rates of boll-opening and defoliation in HWR were the highest. Specifically, the boll-opening rate before defoliation and machine-harvesting in HWR was 44.54 and 5.94% higher on average than in WNR, while the defoliation rate prior to machine-harvesting was 3.45% higher on average than in WNR. The numbers of ineffective defoliated leaves and leaf trash in HWR were the lowest, decreased by 33.40 and 32.43%, respectively, compared with WNR. In conclusion, the HWR planting pattern is associated with a high and stable yield, does not affect fiber quality, promotes early maturation, and can effectively decrease the amount of leaf trash in machine-picked seed cotton, and thus its use is able to improve the quality of machine-harvested cotton.

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Derivation of soil Pb/Cd/As thresholds for safety of vegetable planting: A case study for pakchoi in Guangdong Province, China

LI Fu-rong, WEN Dian, WANG Fu-hua, SUN Fang-fang, WANG Xu, DU Ying-qiong, LIU Xiang-xiang, WAN Kai

2019, 18 (1): 179-189. DOI: 10.1016/S2095-3119(18)61975-6

Abstract （262） PDF in ScienceDirect

Regional guidelines for soil heavy metals, in conjunction with specific crops, are proposed to better assess soil environmental quality. In this study, large amounts of soils with different levels of Pb/Cd/As pollution were collected in Guangdong Province, China, to carry out a pot experiment, which was closer to the actual situation and properties of the heavy metal contaminated soils. Taking the widely planted vegetable pakchoi as the research object, we analyzed the correlations between the Pb/Cd/As concentrations in pakchoi and the total or available soil Pb/Cd/As concentrations and established their optimal regression equations. And then, the total and available soil Pb/Cd/As thresholds for pakchoi were calculated according to the allowable Pb/Cd/As limits in pakchoi and were compared with the current soil assessment standards. Furthermore, a lot of paired vegetable-soil samples in field were collected and their pollution situations were assessed by both the current limit thresholds and the calculated thresholds. Obviously, it was more consistent to assess the Cd and As pollution situation of the vegetable and soil samples with the calculated soil thresholds than the current soil assessment thresholds. It further proved that it was necessary to explore the soil heavy metal thresholds for safety of vegetable in specific regions, which would be more scientific and practical to guide safety production of local agricultural products and effective utilization of soil resources.

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Development of a sensitive and reliable droplet digital PCR assay for the detection of ‘Candidatus Liberibacter asiaticus’

ZHONG Xi, LIU Xue-lu, LOU Bing-hai, ZHOU Chang-yong, WANG Xue-feng

2018, 17 (2): 483-487. DOI: 10.1016/S2095-3119(17)61815-X

Abstract （733） PDF in ScienceDirect

Citrus Huanglongbing (HLB, yellow shoot disease) is one of the most serious citrus diseases worldwide. To better improve the detection sensitivity, a droplet digital PCR (ddPCR) assay was developed for the rapid detection of ‘Candidatus Liberibacter asiaticus’ (Las), the putative causal agent of HLB. The detection of sensitivity comparison using positive plasmid indicated that ddPCR was superior to quantitative PCR (qPCR) for detecting and quantifying Las at low concentrations. The Las detection of 40 field samples also showed that six of 13 asymptomatic samples (46.15%) with high C_t value (>35) were positive by ddPCR. This methodology showed great potential for early HLB infection diagnosis.

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GmDRR1, a dirigent protein resistant to Phytophthora sojae in Glycine max (L.) Merr.

CHEN Qing-shan, YU Guo-long, ZOU Jia-nan, WANG Jing, QIU Hong-mei, ZHU Rong-sheng, CHANG Hui-lin, JIANG Hong-wei, HU Zhen-bang, LI Chang-yu, ZHANG Yan-jiao, WANG Jin-hui, WANG Xueding, GAO Shan...

2018, 17 (06): 1289-1298. DOI: 10.1016/S2095-3119(17)61821-5

Abstract （553） PDF in ScienceDirect

Soil-borne pathogen Phytophthora sojae is an oomycete that causes devastating damage to soybean yield. To mine original resistant genes in soybean is an effective and environmentally-friend approach controlling the disease. In this study, soybean proteins were extracted from the first trifoliolates infected by predominant P. sojae race 1 and analyzed by two-dimensional gel electrophoresis. Nineteen differently-expressed protein spots were detected, and 10 of them were further applied for Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry Assay. One protein containing a dirigent (DIR) domain was identified and belonged to the DIR-b/d family. Therefore, it was named as GmDRR1 (Glycine max Disease Resistance Response 1). Then, GmDRR1 gene was pathologically confirmed to be involved in the resistant to P. sojae in soybean. GmDRR1-GFP (green fluorescent protein) fusion proteins localized in the cell membrane. qRT-PCR results showed GmDRR1 gene expressed differently in P. sojae resistant- and susceptible-soybean cultivars. By the promoter analysis, we found a haplotype H8 was existing in most resistant soybean varieties, while a haplotype H77 was existing in most susceptible soybean varieties. The H77 haplotype had seven SNPs (C to A, G to C, C to A, T to A, T to C, T to C, and T to A) and two single nucleotide insertions. The results supported that the expression difference of GmDRR1 genes between P. sojae resistant- and susceptible-soybean cultivars might depend on the GmDRR1 promoter SNPs. The results suggested that GmDRR1 was a dirigent protein involved in soybean resistant to P. sojae and paved a novel way for investigation of the molecular regulatory mechanism of the defense response to P. sojae in soybean.

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Prevalence and characteristics of extended spectrum β-lactamaseproducing Escherichia coli from bovine mastitis cases in China

YANG Feng, ZHANG Shi-dong, SHANG Xiao-fei, WANG Xu-rong, WANG Ling, YAN Zuo-ting, LI Hong-sheng

2018, 17 (06): 1246-1251. DOI: 10.1016/S2095-3119(17)61830-6

Abstract （524） PDF in ScienceDirect

The aim of the study was to investigate the prevalence and characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from bovine mastitis cases in China. ChromID ESBL agar was used to confirm ESBL-producing E. coli. PCR and DNA sequencing were employed to characterize the genotype of ESBL-producers. Antimicrobial susceptibility was measured by disc diffusion. Overall, 73 of 318 E. coli isolates (22.96%) were identified as ESBL-producers. Of these ESBL-producing E. coli, the prevalence of bla_CTX-M and bla_TEM-1 was 97.26 and 71.23%, respectively. The predominant CTX-M-type ESBL was CTX-M-15 (65.75%), followed by CTX-M-14 (10.96%), CTX-M-55 (9.59%), CTX-M-64 (5.48%), CTX-M-65 (4.11%) and CTX-M-3 (1.37%). This study is the first report of CTX-M-64 and CTX-M-65 in E. coli isolated from bovine mastitis. Furthermore, 72 ESBL-producing E. coli isolates (98.63%) were found to be multidrug-resistance. This study noted high prevalence and rates of antimicrobial resistance of ESBL-producing E. coli isolates from bovine mastitis cases in China.

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Penicillin-resistant characterization of Staphylococcus aureus isolated from bovine mastitis in Gansu, China

YANG Feng, LIU Long-hai, WANG Ling, WANG Xu-rong, LI Xin-pu, LUO Jin-yin, ZHANG Zhe, ZHANG Shi-dong, YAN Zuo-ting, LI Hong-sheng

2017, 16 (08): 1874-1878. DOI: 10.1016/S2095-3119(16)61531-9

Abstract （1414） PDF in ScienceDirect

Bovine mastitis caused by Staphylococcus aureus is difficult to treat because of increasing resistance against antibiotics, especially penicillin. β-Lactamase and biofilm are responsible for penicillin resistance of S. aureus. The aim of this study was to investigate the β-lactamase activity and biofilm formation capacity of 37 penicillin-resistant S. aureus strains (35 were blaZ positive and 2 were blaZ negative) from bovine mastitis in Gansu Province, China, as well as to measure the intercellular adhesion genes icaA and icaD of these strains. β-Lactamase Test Kit was used to determine the β-lactamase activity, biofilm formation was tested by semi-quantitative adherence assay method. Moreover, the presence of icaA and icaD were measured by PCR. A total of 32 penicillin-resistant S. aureus strains, including the two blaZ-negative strains, were identified as β-lactamase producers. All tested S. aureus isolates produced biofilm in the microtiter plate assay. Meanwhile, all these strains were PCR-positive for the ica locus, icaA and icaD. The study indicated high prevalence of β-lactamase activity, biofilm-forming capacity, and the ica genes among the penicillin-resistant S. aureus isolates, and implied that S. aureus resistant to penicillin was attributed to multiple mechanisms.

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Field evaluation of Streptomyces rubrogriseus HDZ-9-47 for biocontrol of Meloidogyne incognita on tomato

JIN Na, XUE Hui* LI Wen-jing, WANG Xue-yan, LIU Qian, LIU Shu-sen, LIU Pei, ZHAO Jian-long, JIAN Heng

2017, 16 (06): 1347-1357. DOI: 10.1016/S2095-3119(16)61553-8

Abstract （814） PDF in ScienceDirect

Streptomyces rubrogriseus HDZ-9-47, isolated from eggs of Meloidogyne spp., was evaluated as a potential biocontrol agent of Meloidogyne incognita under in vitro and protective field. Microscopic observations showed that HDZ-9-47 parasitized eggs of M. incognita within 7 days. In vitro, the culture filtrate of HDZ-9-47 caused 97.0% mortality of second-stage juveniles (J2s) of M. incognita and inhibited more than 50% egg hatching. In the field, compared with the control, the root-knot index and J2s density in the treatment of drench the broth contained 10¹² HDZ-9-47 spores were respectively reduced by 51.1 and 80.7% at 90 days post transplantation, which were better than that in other application doses and methods. In addition, reduction rates of root-knot index and J2s density of the treatment of combined application of HDZ-9-47 with biofumigation was 87.1 and 91.0%, respectively, better than either of HDZ-9-47 or biofumigation used alone or fosthiazate treatment. And tomato yield also increased by 16.1%. Together, our results suggest that HDZ-9-47 could be an effective biocontrol agent of M. incognita, and that application of HDZ-9-47 combined with cabbage residue biofumigation was a promising and sustainable option for M. incognita control.

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Development of glyphosate-tolerant transgenic cotton plants harboring the G2-aroA gene

ZHANG Xiao-bing, TANG Qiao-ling, WANG Xu-jing, WANG Zhi-xing

2017, 16 (03): 551-558. DOI: 10.1016/S2095-3119(16)61458-2

Abstract （813） PDF in ScienceDirect

Given that glyphosate weed control is an effective strategy to reduce costs and improve economic outcomes of agricultural production in China, the development of glyphosate-resistant cotton holds great promise. Using an Agrobacterium-mediated transformation method, a new G2-aroA gene that encodes 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) was transformed into cotton cultivar K312. The transgenic cotton plants were regenerated from a callus tissue culture via kanamycin selection. Ten regenerated cotton plants were obtained and allowed to flower normally to produce fruit. The results from polymerase chain reaction (PCR) and Southern and Western blot analyses indicated that the target gene was integrated into the cotton chromosome and was expressed effectively at the protein level. The glyphosate tolerance analysis showed that the transgenic cotton had a high resistance to glyphosate. Further, even cotton treated with 45.0 mmol L^–1 of glyphosate was able to slowly grow, bloom and seed. The transgenic cotton may be used for cotton breeding research of glyphosate-tolerant cotton.

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Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China

YU Yun-qi, WU Qiong, SU Hua-nan, WANG Xue-feng, CAO Meng-ji, ZHOU Chang-yong

2017, 16 (02): 503-508. DOI: 10.1016/S2095-3119(16)61533-2

Abstract （1164） PDF in ScienceDirect

To identity the potential pathogen associated with the yellow vein clearing symptom on lemon trees, the profiles of virus-derived small interfering RNAs from citrus samples were obtained and analyzed by deep sequencing method in this study. Twenty-seven contigs almost cover the full length genome of Citrus yellow vein clearing virus (CYVCV) isolate YN were obtained using the small RNA deep sequencing technology. Analysis showed that this isolate CQ shared the highest nucleotide identity with isolate Y1 (JX040635) and YN (KP313242), both of which belong to the genus Mandarivirus in the family Alphaflexiviridae. Mapping analysis of viral-derived siRNA (vsiRNA) profiles revealed an uneven distribution pattern of their generations along both positive and negative genome strands, and 22- and 21-nt vsiRNAs ranked the majority. BLAST against viroids and other viral databases confirmed that this sample was single-infected only by CYVCV, which indicated that CYVCV was the exact causal agent for the yellow clearing symptom occurring on lemon. This is the first CYVCV isolate detected in Chongqing and the second in China. This result could provide a molecular basis for the investigation of citrus viral diseases to protect citrus health in this region.

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Genetic characterization of antimicrobial resistance in Staphylococcus aureus isolated from bovine mastitis cases in Northwest China

YANG Feng, WANG Qi, WANG Xu-rong, WANG Ling, LI Xin-pu, LUO Jin-yin, ZHANG Shi-dong, LI Hong-sheng

2016, 15 (12): 2842-2847. DOI: 10.1016/S2095-3119(16)61368-0

Abstract （1119） PDF in ScienceDirect

Staphylococcus aureus is the most common etiological pathogen of bovine mastitis. The resistant strains make the disease difficult to cure. The aim of this study was to characterize the genetic nature of the antimicrobial resistance in S. aureus cultured from bovine mastitis in Northwest China in 2014. A total of 44 S. aureus were isolated for antimicrobial resistance and resistance-related genes. Antimicrobial resistance was determined by disc diffusion and the corresponding resistance genes were detected by PCR. Phenotype indicated that S. aureus isolates were resistant to penicillin (84.09%), erythromycin (20.45%), tetracycline (15.91%), gentamicin (9.09%), tobramycin (6.82%), kanamycin (6.82%) and methicillin (2.27%). 9.09% of the S. aureus isolates were classified as multidrug resistant. In addition, genotypes showed that the isolates were resistant to rifampicin (100%, rpoB), penicillin (95.45%, blaZ), tetracycline (22.73%, tetK, tetM, alone or in combination), erythromycin (22.73%, ermB or ermC), gentamicin/tobramycin/kanamycin (2.27%, aacA-aphD), methicillin (2.27%, mecA) and vancomycin (2.27%, vanA). Resistance to tetracycline was attributed to the genes tetK and tetM (r=0.558, P<0.001). This study noted high-level geno- and phenotypic antimicrobial resistance in S. aureus isolates from bovine mastitis cases in Northwest China.

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The third-party regulation on food safety in China: A review

ZHANG Man, QIAO Hui, WANG Xu, PU Ming-zhe, YU Zhi-jun, ZHENG Feng-tian

2015, 14 (11): 2176-2188. DOI: 10.1016/S2095-3119(15)61114-5

Abstract （1836） PDF in ScienceDirect

Stakeholders in the field of food safety management in China can be classified into three categories, government, food producers (farmers and enterprises), and the third-party regulatory bodies. The third-party regulation has experienced rapid development in past twenty years, and recently received considerable attention from consumers and the central government. This paper provides a review about the development, problems and future trend of the third-party regulation on food safety in China. To be specific, five forms of the third-party regulation are assessed, including media exposure, the third-party certification, regulation by consumer associations, social movements promoted by non-governmental organizations (NGOs), and regulation by industry associations. The study concludes that media and consumer associations are the major players in the third-party regulation and are highly repudiated among customers. The food certification industry has developed rapidly, but is now facing crises of confidence among consumers because of its lack of self-regulation. NGOs and industry associations still remain in the early development stages of food safety management, and therefore, are of little importance in current regulatory bodies.

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High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’

WANG Xue-feng, CHEN Jiao-yue, TAN Jin , DUAN Suo, DENG Xiao-ling, CHEN Jian-chi, ZHOU Chang-yong

2015, 14 (10): 2002-2010. DOI: 10.1016/S2095-3119(14)60979-5

Abstract （1434） PDF in ScienceDirect

Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the first time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, São Paulo isolates and a few Florida isolates.

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Spatiotemporal Changes in Soil Nutrients: A Case Study in Taihu Region of China

LIU Lei-lei, ZHU Yan, LIU Xiao-jun, CAO Wei-xing, XU Mao, WANG Xu-kui , WANG En-li

2014, 13 (1): 187-194. DOI: 10.1016/S2095-3119(13)60528-6

Abstract （1558） PDF in ScienceDirect

The accurate assessment of the spatiotemporal changes in soil nutrients influenced by agricultural production provides the basis for development of management strategies to maintain soil fertility and balance soil nutrients. In this paper, we combined spatial measurements from 2 157 soil samples and geostatistical analysis to assess the spatiotemporal changes in soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AP) and available potassium content (AK) from the first soil survey (in the 1980s) to the second soil survey (in the 2000s) in the Taihu region of Jiangsu Province in China. The results showed that average soil nutrients in three soil types all exhibited the increased levels in the 2000s (except for AK in the yellow brown soil). The standard deviation of soil nutrient contents increased (except for TN in the paddy soil). Agricultural production in the 20 years led to increases in SOC, TN, AP and AK by 74, 82, 89 and 65%, respectively, of the Taihu areas analyzed. From the 1980s to 2000s all the nugget/sill ratios of soil nutrients indices were between 25 and 75% (except for AK in the yellow brown soil in the 2000s), indicating moderate spatial dependence. The ratio of AP in the yellow brown soil in the 2000s was 88.74%, showing weak spatial dependence. The spatial correlation range values for SOC, TN, AP and AK in the 2000s all decreased. The main areas showing declines in SOC, TN and AP were in the northwest. For AK, the main region with declining levels was in the east and middle of western areas. Apparently, the increase in soil nutrients in the Taihu region can be mainly attributed to the large increase in fertilizer inputs, change in crop systems and enhanced residues management since the 1980s. Future emphasis should be placed on avoiding excess fertilizer inputs and balancing the effects of the fertilizers in soils.

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Agricultural Market Name Geo-Locating System Based on an Administrative Ontology and Web Search Engine

HU Yi-min, SONG Liang-tu, WEI Yuan-yuan, HUANG He, WANG Xue

2012, 11 (5): 849-857. DOI: 10.1016/S1671-2927(00)8607

Abstract （1222） PDF in ScienceDirect

The problem of associating the agricultural market names on web sites with their locations is essential for geographical analysis of the agricultural products. In this paper, an algorithm which employs the administrative ontology and the statistics from the search results were proposed. The experiments with 100 market names collected from web sites were conducted. The experimental results demonstrate that the algorithm proposed obtains satisfactory performance in resolving the problem above, thus the effectiveness of the method is verified.

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From Web Resources to Agricultural Ontology: a Method for Semi-Automatic Construction

WEI Yuan-yuan, WANG Ru-jing, HU Yi-min, WANG Xue

2012, 11 (5): 775-783. DOI: 10.1016/S1671-2927(00)8599

Abstract （1519） PDF in ScienceDirect

In recent years, with the rapid development of information science, ontology becomes a popular research topic in the fields of knowledge engineering and information management. The reason for ontology being so popular is in large part due to what they promise: a shared and common understanding of some domain that can be communicated across people and computers. In the field of agriculture, FAO has started up the Agricultural Ontology Service (AOS) study project since 2001, AOS aims at providing knowledge service by agricultural domain ontology, it is the new seedtime for agricultural information service. However, establishing the ontology necessitates a great deal of expert assistance; manually setting it up would entail a lot of time, not to mention that there are only a handful of experts available. For this reason, using automatic technology to construct the ontology is a subject worth pursuing. A semi-automatic construction method for agricultural professional ontology from web resources is presented in this paper. For semi-structured web pages, the method automatically extracted and stored structured data through a program, built pattern mapping between relational database and ontology through human-computer interaction, and automatically generated a preliminary ontology, finally completed checking and refining by domain experts. The method provided a viable approach for ontology construction based on network resources in the actual work.

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Insecticidal Constructure and Bioactivities of Compounds from Ficus sarmentosa var. henryi

WANG Xue-gui, WEI Xiao-yi, HUANG Xing-yan, SHEN Li-tao, TIAN Yong-qing , XU Han-hong

2011, 10 (9): 1402-1409. DOI: 10.1016/S1671-2927(11)60133-8

Abstract （1877） PDF in ScienceDirect

Insecticidal activities of the petroleum ether-, chloroform-, ethyl acetate-, and water-soluble fractions of the methanolicextract of Ficus sarmentosa var. henryi were assayed against Musca domestica adults. The chloroform- and ethyl acetatesolublefractions were the most active with 92.6 and 88.9% mortalities (24 h after treatment) respectively. Therefore, thetwo fractions were combined and four compounds, isolated from the fractions by activity-guided fractionation, wereelucidated as 7-hydroxycoumarin, apigenin, eriodictyol, and quercetin by spectroscopic method and displayed excellentinsecticidal activities against adults of M. domestica and 4th instar larva of Aedes albopictus. Among those, 7-hydroxycoumarin showed the strongest insecticidal activities with lethal concentrations (LC50) values of 72.13 μg g-1sugar and 4.87 μg mL-1 (48 h after treatment) against the test insects respectively. The cytoxicities of these compounds onBTI-Tn-5B1-4 cell were also investigated for the insecticidal mechanism and found that quercetin represented superiorinhibitory activity with MTT assay and reactive oxygen species (ROS) against BTI-Tn-5B1-4 cell, but slightly weaker thanthat of the positive control (azadirachtin) and significantly greater than the negative control (DMSO only). Meanwhile,eriodictyol demonstrated the strongest effect on the mitochondrial membrane potentials (MMP). In conclusion, based ontheir comparative toxicities to commercial insecticides and their cytotoxic effects, some of the compounds from theF. sarmentosa have potential as botanical insecticides.

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The Responses of Morphological Trait, Leaf Ultrastructure, Photosynthetic and Biochemical Performance of Tomato to Differential Light Availabilities

FU Qiu-shi, ZHAO Bing, WANG Xue-wen, WANG Yu-jue, REN Shu-xin , GUO Yang-dong

2011, 10 (12): 1887-1897. DOI: 10.1016/S1671-2927(11)60189-2

Abstract （3189） PDF in ScienceDirect

The whole-plant morphology, leaf ultrastructure, photosynthesis as well as enzyme activities of two tomato cultivars (Meifen-2 and Hongsheng) to differential light availabilities (450-500 μmol m-2 s-1, 75-100 μmol m-2 s-1) were examined in controlled environment. The results showed that the plant biomass and root/shoot ratio decreased and the specific leaf area increased significantly under the low light condition. There was a significant increase in malondialdehyde (MDA) concentration, superoxide dismutase (SOD) and peroxidase (POD) activities and decrease in soluble sugar and protein contents in LL-grown plants. For both cultivars, downregulation of photosynthesis and electron transport components were observed in LL-grown plants, the inhibition of the photosynthesis under the LL condition could be partially explained by the decrease of stomata density and by the changes of chloroplast.

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