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本期目录
2019 Vol. 27, No. 12 Published: 20 November 2019
Articles and Letters
Cloning and Expression Analysis of Disease-related Gene
SiRAR1
in Foxtail Millet (
Setaria italica
)
BAI Hui, SONG Zhen-Jun, SONG Dan-Dan, WANG Yong-Fang, QUAN Jian-Zhang, DONG Zhi-Ping, LI Zhi-Yong
2019, 27(12): 2091-2100 |
doi:
10.3969/j.issn.1674-7968.2019.12.001 | Full text
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Abstract
Required for
Mla12
-required resistance (
RAR1
) as an important element for plant disease resistance, is widely involved in plant resistance response. To study the structure and expression characteristics of
SiRAR1
in foxtail millet (
Setaria italica
), the CDS sequence and promoter sequence of
SiRAR1
gene were separately cloned with the leaf cDNA and genomic DNA from resistance material 'Shilixiang' as template by PCR, and the biological characteristics of SiRAR1 were predicted by bioinformatics analysis. Then the expression patterns of
SiRAR1
in different tissues and the
Uromyces setariae
-
italicae
-induced stress response were surveyed by qRT-PCR, respectively. Lastly the prokaryotic expression characteristics for the gene were detected by SDS-PAGE. The results showed that the ORF of
SiRAR1
gene contained 765 bp and encoded 254 amino acids (GenBank No. MK814879). The predicted protein molecular weight was 28.04 kD and the theoretical isoelectric point (
pI
) was 8.13. The largest secondary structure element of SiRAR1 protein was random coil, and the smallest was beta turn. Phylogenetic analysis showed that SiRAR1 protein had the closest evolutionary relationship with plants in the same family, and had the highest genetic homology (92.44%) with the hypothetical protein C2845_PM12G15490 (RLM79685.1), a gene from chromosome 12 of
Panicum miliaceum
. The qRT-PCR analysis showed that
SiRAR1
gene was expressed in roots, stems, leaves and panicles in foxtail millet. There was the highest expression level in roots and the lowest in stems, and the expression levels of
SiRAR1
were similar in panicles at booting and heading stages. The qRT-PCR analysis also showed that under the infection of
Uromyces setariae
-
italicae
, the expression level of
SiRAR1
gene in the resistant material 'Shilixiang' was up-regulated from 12 to 36 h and peaked at 36 h, and up-regulated at 96 h in the susceptible material 'Yugu1'. The peak expression of
SiRAR1
gene in 'Shilixiang' was about 3 times higher than that in 'Yugu1' (
P
<0.01), and its peak expression in 'Yugu1' was about 1.6 times higher than that in 'Shilixiang' (
P
<0.05). The results showed that the expression of
SiRAR1
gene had earlier up-regulated time, longer duration and stronger up-regulated range in resistant plants than that in susceptible plants. The prokaryotic expression vector pET30a-
SiRAR1
was induced to express SiRAR1 fusion protein with 33 kD by 0.1 and 0.4 mmol/L isopropyl β-D-thiogalactoside (IPTG), respectively. The results provide a theoretical foundation for further study on the
SiRAR1
function and its disease resistance mechanism in foxtail millet.
Microsatellite Genetic Diversity of Seven Loach (
Misgurnus anguillicaudatus
) Populations in China
LIU Jie, GAO Feng-Ying, LU Mai-Xin, CHEN Gang, CAO Jian-Meng, LIU Zhi-Gang, WANG Miao
2019, 27(12): 2101-2109 |
doi:
10.3969/j.issn.1674-7968.2019.12.002 | Full text
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Abstract
Due to environmental pollution and human activities, the amount of loach resources in China has been sharply reduced, and germplasm resources have been degraded. In order to explore the genetic diversity and population genetic structure of different geographical populations of loach (
Misgurnus anguillicaudatus
) in China, 10 microsatellite markers were used to analyze the genetic diversity of 7 populations in Poyang Lake region and Pearl River Basin of China (Poyang Lake, Yingde, Qingyuan, Liannan, Nanxiong, Meizhou, Liuzhou). The results showed that the average number of allele (
Na
) and effective allele (
Ne
) per locus were 7 and 2.5, and the average observed heterozygosity (
Ho
) and expected heterozygosity (
He
) were 0.327 4 and 0.396 0. The average population inbreeding coefficient (
Fis
), genetic differentiation coefficient (
Fst
) and number of migrants per generation (
Nm
) of the 7 loach populations were 0.093 0, 0.372 0 and 0.422 1, indicating that the level of genetic exchange among the 7 populations was low and there was a high degree of genetic differentiation. A total of 79 alleles were amplified in 10 pairs of microsatellite primers, the
Na
,
Ne
,
Ho
,
He
and polymorphic information content (
PIC
) ranged from 3.0 to 7.5, 1.7 to 5.5, 0.307 4 to 0.534 7, 0.329 0 to 0.861 5, and 0.316 8 to 0.529 4, respectively. The genetic distance between the 7 loach populations was 0.045 3~1.602 3. The genetic relationship of Liuzhou and Nanxiong population showed the closest with lowest distance of 0.045 3, while the genetic relationship of Qingyuan and Meizhou population showed the farthest with highest distance of 1.602 3. The clustering analysis based on genetic distance showed that the Liuzhou, Nanxiong, Liannan and Meizhou populations were clustered into one branch, while the Qingyuan, Yingde and Poyang Lake populations were clustered into another branch. Above results demonstrated that the level of genetic diversity in loach in China was moderate and the genetic differentiation among loach populations was affected by factors such as self-migration ability and geographical isolation. This study provides a theoretical basis for further selection of the basic group of loach fine breeds and the protection of loach germplasm resources.
Cloning and Expression Analysis of
DcPSY2
Gene Under Abiotic Stress in Carrot (
Daucus carota
)
DING Xu, WANG Ya-Hui, LI Tong, ZHANG Rong-Rong, XU Zhi-Sheng, XIONG Ai-Sheng
2019, 27(12): 2110-2119 |
doi:
10.3969/j.issn.1674-7968.2019.12.003 | Full text
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Abstract
Carotenoids, as an important nutrient, are very common in carrot (
Daucus carota
). Lycopene, a kind of carotenoids, plays important roles in growth, development, and response to abiotic stress in higher plant. Phytoene synthase (PSY) is one of the key enzymes of lycopene biosynthesis. In this study,
DcPSY2
(GenBank No. NM_001329167.1) was cloned from carrot cv. 'Junchuanhong' by RT-PCR (reverse transcription PCR). It contained an ORF with the length of 1 317 bp and encoded 438 amino acids. The amino acid sequences of DcPSY2 and the PSY proteins of 17 other plants were compared, the results showed that the overall similarity of PSY proteins was 82.22 %, which indicated that PSY proteins were conserved. Evolutionary relationship exhibited that DcPSY2 protein had the closest evolutionary relationship with the PSY protein in mahogany (
Bixa orellana
). DcPSY2 protein was a hydrophilic and non-secretory protein without signal peptide. It belonged to isoprenoid biosyn C1 superfamily and was distributed in various organelles. Secondary structure prediction demonstrated that DcPSY2 contained 53.65 % α-helix, 5.48 % β-fold, 12.79 % extended main chain and 28.08 % random curl. The results of qRT-PCR showed that
DcPSY2
gene expression changed significantly in response to 4 kinds of abiotic stresses, including high temperature (38 ℃), low temperature (4 ℃), drought (200 g/L PEG6000) and high salt (200 mmol/L NaCl). Under high temperature or high salt treatments, the relative expression level of
DcPSY2
reached the peak after 2 h. Whereas under low temperature or drought treatments, the expression level of
DcPSY2
increased significantly at 1 h (
P
<0.05). The results provide a basic material for the functional study of
DcPSY2
gene in carrot growth and its application study in stress resistance breeding.
Resistance Allelism Study of Chinese Cabbage (
Brassica campestris
spp.
pekinensis
)
Turnip mosaic virus
Disease
MAN Wei-Ping, ZHANG Zhi-Gang, LIU Shuan-Tao, WANG Rong-Hua, WANG Li-Hua, XU Nian-Fang, XU Wen-Ling, LIU Xian-Xian, LIU Chen, LI Qiao-Yun, ZHAO Zhi-Zhong
2019, 27(12): 2120-2129 |
doi:
10.3969/j.issn.1674-7968.2019.12.004 | Full text
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Abstract
Chinese cabbage (
Brassica rapa
spp.
pekinensis
) originated in China, and is an important vegetable in China and even in East Asia. Virus disease is one of the most important diseases for Chinese cabbage production, in which
Turnip mosaic virus
(TuMV) is the main pathogen. The inheritance pattern for TuMV resistance is very complicated in Chinese cabbage. In order to better understand the similarities and differences of resistance sites between different TuMV resistant materials, the high-generation inbred line TuMV resistant material '73' and National TuMV source resistant material '8407' were used as core parents to study the similarities and differences of TuMV resistant sites in 9 resistant materials ('73', '8407', 'Zao 219', '07-372', C07-14', 'Henan 304', '322', '826' and '07-55'). By crossing and inbreeding, F
1
and F
2
populations of 'Zao219'×'8407', '07-372'×'8407', '07-14'×'8407', 'Henan304'×'8407', '322'×'8407', '826'×'8407', '07-55'×'8407', '73'×'8407', 'Zao219'×'73', '07-372'×'73', 'Henan304'×'73', '322'×'73', '07-55'×'73', '07-372'×'322', 'Henan304'×'322', '07-372'×'Henan304', 'Zao219'×'322', 'Zao219'×'Henan304' and 'Zao219'×'07-372' were constructed. The C4 strains of TuMV was inoculated on the above F
1
, F
2
and parent materials. The similarities and differences of resistance sites among different combinations were judged according to the resistance performance of F
1
and the resistance isolation of F
2
. The results showed, in combinations '73'×'8407' and '322'×'8407', both F
1
were resistant, individual susceptible plants were found in both F
2
populations, indicating that the resistance sites in '73' and '322' were linked to that in '8407' but not allelic. In combination '07-55'×'8407', F
1
was resistant, no susceptible plants were found in F
2
, but 3 grade 1 and 6 grade 3 plants, indicated that the resistance site in '07-55' and '8407' were incomplete allelic, should be linked. In combinations '322'×'73' and '07-55'×'73', F
1
and all of F
2
plants were resistant, no susceptible plants were found in F
2
, indicating that the resistance sites of '322', '07-55' and '8407' were allelic, and their resistance was controlled by the same gene. In combinations 'Zao219'×'8407', '07-372'×'8407', '07-14'×'8407', and '826'×'8407', all of the F
1
and F
2
plants were resistant, no susceptible plants were found in F
2
, indicating that the resistance sites of 'Zao219', '07-372', '07-14', '826' and '8407' were allelic, and their resistance were controlled by the same gene. In combination 'Henan304'×'8407', F
1
was susceptible, both resistant and susceptible plants were found in F
2
, and the segregation ratio of resistant and susceptible plants was 9∶7, indicating that the resistance sites of 'Henan304' and '8407' were not allelic, TuMV resistant genes in 'Henan304' and '8407' were complementary. In combination 'Henan304'×'322', F
1
was resistant, both resistant and susceptible plants were found in F
2
, and the segregation ratio of resistant and susceptible plants was 15∶1, indicated that the resistance sites of 'Henan304' and '322' were not allelic, TuMV resistant genes in 'Henan304' and '322' were inherited independently. This result provides a basis for the next step of targeted selection of disease resistant materials and research on the molecular markers of resistance to TuMV in Chinese cabbage. It also broadens the germplasm resources of resistance of Chinese cabbage for TuMV resistant breeding, and provides theoretical guidance for the selection of parents and offspring of resistance breeding of Chinese cabbage to TuMV.
Bioinformatics Analysis, Subcellular Localization and Expression Analysis of
OsERF103
Gene in Rice (
Oryza sativa
)
ZOU Jie, LI Sheng-Qiang, LIU Xian-Jun, CHEN Gang
2019, 27(12): 2130-2139 |
doi:
10.3969/j.issn.1674-7968.2019.12.005 | Full text
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Abstract
Ethylene responsive factors (ERFs) are plant-specific transcription factors that play important roles in plant developmental process and in response to abiotic stress. In order to explore the function of
OsERF103
(GenBank No. XM_015768788) in rice (
Oryza sativa
) , bioinformatics methods were used to analyze the sequence characteristic of
OsERF103
. For subcellular localization analysis, the fusion expression vector of pBWA(V)HS-
OsERF103
-Glosgfp was constructed and transformed into rice protoplast, then laser scanning confocal microscopy was used to observe the subcellular localization of OsERF103 fusion protein in rice protoplast; Expression analysis of
OsERF103
in different tissues and under different abiotic stress conditions was conducted by qRT-PCR. The results showed that OsERF103 was a hydrophilic and unstable protein without signal peptide and transmembrane structure, and contained an AP2 (APETALA2) domain. Phylogenetic analysis revealed the OsERF103 was evolutionarily closest to a abscisic acid repressor 1-like (ABR1-like) protein of
Oryza brachyantha
. The results of subcellular localization showed that OsERF103 was located in the nucleus.
OsERF103
transcripts were detected in all sampled tissues at booting stage, with the highest level detected in root and weak level detected in leaf and young spike.
OsERF103
transcripts were induced by high temperature, low temperature, PEG6000, high salt and abscisic acid (ABA), and differential expression patterns of
OsERF103
were showed under the different treatment conditions. This study provides basic data for further exploring the biological function of
OsERF103
.
Transcriptome Analysis of Large-fruit Mutant During the Early Development of Fruit in 'Tonami' Apple (
Malus domestica
)
ZHANG Xue-Ying, LI Zhen-Xia, YIN Bao-Ying, LI Zhong-Yong, ZHANG Yuan, XU Ji-Zhong, LI Qi-Wei, SHAO Jian-Zhu
2019, 27(12): 2140-2149 |
doi:
10.3969/j.issn.1674-7968.2019.12.006 | Full text
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Abstract
The 'Tonami' large-fruit mutant derived from the natural mutant of 'Tonami' apple. To analysis the reason of large-fruit mutant of 'Tonami' apple (
Malus domestica
'Tonami'), fruit size, cell ploidy, cellular structure and transcriptome in the early development of fruit were studied in 'Tonami' apple and its large-fruit mutant. Results showed that weight of average single fruit of 'Large-fruit Tonami' apple was significantly higher than the contrast (
P
<0.05), was 1.5 times of the contrast. There was no significant difference in the cell size of the fruits, but the number of cells in the 'Large-fruit Tonami' at 28 d after full bloom and at the ripeness was significantly higher than that of 'Tonami' (
P
<0.05). Cell ploidy were the same of 'Large-fruit Tonami' apple and contrast. Transcriptome of fruit after full bloom 14 and 28 d were compared with 'Tonami' and 'Large-fruit Tonami' apple. Fifty-one differential expressed genes (DEGs) were identified. By KEGG analysis, these unigenes were found to be implicated in plant hormone signal transduction pathway. Five genes that might be related to large-fruit mutant were selected from that pathway, these genes were mainly involwed in cytokinin signaling transduction pathway and ethylene signaling transduction. The study showed that large-fruit mutant of 'Tonami' apple might be related to the changes of plant hormones in fruit development. This study would provide basic information for further studying the cytological and molecular basis on apple large-fruit mutant.
Identification and Expression Analysis of SnRK2 Gene Family in Strawberry (
Fragaria vesca
)
LIU Tao, WANG Ping-Ping, HE Hong-Hong, LIANG Guo-Ping, GAO Xue-Qin, LU Shi-Xiong, CHEN Bai-Hong, MAO Juan
2019, 27(12): 2150-2163 |
doi:
10.3969/j.issn.1674-7968.2019.12.007 | Full text
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Abstract
SnRK2 (sucrose non-fermenting-1-related protein kinase) is a kind of plant-specific Ser/Thr protein kinase, which plays an important role in plant stress resistance. In order to explore the number, structure and expression difference of SnRK2 gene family of strawberry (
Fragaria vesca
) in response to abiotic stress, based on the conserved sequences of
SnRK2
genes in
Arabidopsis thaliala
and rice (
Oryza sativa
).Using bioinformatic tools, the homologous comparison, gene structure, systematic evolution, conserved motif, physical and chemical properties of protein, protein secondary structure and sequential action elements of strawberry SnRK2 gene family were analyzed, and qRT-PCR was used to analyze the gene expression under simulated stress. Ten members of SnRK2 gene family were identified from strawberry genome database, divided into 3 subfamilies, the number of coding amino acids is 258~366, and the molecular weight was 29 469.75~41 481.68 D, the theoretical isoelectric points were between 4.68 and 9.10, which were distributed on 4 chromosomes of strawberry. Gene structure and motif analysis showed that most genes had 9 exons, and the distribution of motif in the same subfamily was basically similar. The results of subcellular localization prediction showed that FvSnRK2 gene family was mainly expressed in cytoplasm. The secondary structures of protein were mainly α-helix and irregular curl. Analysis of the upstream 2 kb cis-acting element found that all members of the FvSnRK2 gene family contain MYB and MYC transcription factor response elements. The results of qRT-PCR analysis showed that the relative expression of 5 genes in FvSnRK2 gene family reached the peaks at 12 h after 10 % PEG6000 processing, and the response of
FvSnRK2.4
was the most obvious, which was 15 times higher than that at 0 h. After 100 μmol/L ABA (abscisic acid) treatment, the relative expression of 6 genes was the highest at 24 h, and 2 genes had the highest relative expression at 12 h,
FvSnRK2.5
and
FvSnRK2.9
responsed strongly, which were 16.2 times and 42.4 times higher than that at 0 h, respectively. The relative expression of 7 genes was highest at 2 h after 200 mmol/L NaCl treatment, the response of
FvSnRK2.10
was 65.2 times higher than that at 0 h, and
FvSnRK2.5
was the highest at 12 h, which was 94.7 times higher than that at 0 h.
FvSnRK2.5
and
FvSnRK2.10
had strong response after ABA and NaCl treatment, and played important roles in stress resistance signal regulation in strawberry. The present research provides theoretical reference for functional verification and breeding of strawberry
SnRK2
gene.
Cloning and Expression Analysis of
LsMYB5
Gene in
Lycoris sprengeri
HOU Shuo, GAO Yan-Hui, TONG Zai-Kang
2019, 27(12): 2164-2174 |
doi:
10.3969/j.issn.1674-7968.2019.12.008 | Full text
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Abstract
Lycoris sprengeri
is perennial herbaceous plants of Amaryllidaceae,
Lycoris
with the red and blue multicolor flower, which is a good material for cut flower, potted flower and landscape gardening, so
L. sprengeri
has the very high commercial value. To enrich the germplasm resources and cultivate varieties in
L. sprengeri
, a R2R3-MYB transcription factor gene
LsMYB5
cDNA sequence (GenBank No. MK779710) was successfully screened by using reverse transcription PCR (RT-PCR) and rapid amplification of cDNA ends (RACE). The
LsMYB5
gene length was 871 bp, and the open reading frame (ORF) was 681 bp, which encoded 226 amino acids. The c-terminal of LsMYB5 protein contained conservative EAR inhibition domain (pdLNLD/ELxiG/s) and zinc finger domain (CX-(1-2), CX-(7-12), CX-(1-2)C), which may have transcriptional inhibition function.
LsMYB5
gene mainly expressed in leaves and the fading period of petals, and there were significant differences in the expression of
LsMYB5
in clones with different colors (
P
<0.05). To further analyze
LsMYB5
gene function, prokaryotic expression vector of pET-30(a)-
LsMYB5
was constructed and transformed into
Escherichia coli
BL21 (DE3), the expression of recombinant proteins was induced under the induction of isopropyl glucosinolates galactose glucoside (IPTG), and the His label protein was purified. The results will provide the theory basis for screening structural genes regulated by LsMYB5 transcription factor. which related to flower color formation in
Lycoris sprengeri
.
Construction and Analysis of Suppression Subtractive Library of Wild Drought-tolerant Crowtoe (
Lotus corniculatus
) Under Drought Stress
JIAN Zhong-Ling, ZHAO Li-Li, WANG Pu-Chang, SUN Xiao-Fu, CHEN Chao
2019, 27(12): 2175-2187 |
doi:
10.3969/j.issn.1674-7968.2019.12.009 | Full text
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267
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Abstract
Crowtoe (
Lotus corniculatus
) is a legume forage with broad application prospects, but the efficiency of promotion and utilization is seriously affected by drought. In order to solve this problem, after many years of research, the high drought tolerance crowtoe germplasm B08 was selected by this team, finally. In order to further study and explore the drought-resistance mechanism of germplasm B08, suppression subtractive hybridization (SSH) technology was used to construct the positive and negative SSH cDNA library of B08 under drought stress. 600 positive clones were randomly selected from the forward and reverse libraries for sequencing analysis. The results showed that: (1) 574 and 595 high quality sequences were obtained in the forward and reverse libraries, with an average length of 207.5 bp and 242.7 bp, respectively. Finally, 632 unigenes sequences were obtained by assembling high quality sequence data, of which 178 were forward library and 454 reverse library. (2) The 632 unigenes were compared with public databases by BLAST, and 147 genes were annotated successfully. Among them, 80 were known genes, 67 were unknown genes, and 485 new genes were found. (3) The results of NCBI Non-Redundant Protein Sequence Database (nr) annotation showed that there were high homology with
Populus trichocarpa
,
Malus domestica
,
Spinacia oleracea
,
Hordeum vulgare
,
Brassica napus
,
Cajanus cajan
,
Cicer arietinum
,
Coffea canephora
and so on. The forward and reverse libraries were classified using Gene Ontology (GO) program. The genes involved in cell, cell part, organcell, binding, metabolic process, and catalytic activity, cellular process accounted for a large proportion. (4) The obtained unigenes involved the synthesis of plant photosynthesis, energy metabolism, hormone synthesis, protein metabolism, nucleic acid metabolism, ion transport and signal transduction. (5) Substances closely related to drought resistance of plants had been found, such as serine/threonine-protein phosphatase, calmodulin-like protein (CML), indole-3-acetic acid-induced protein ARG7, mitogen-activated protein kinase (MAPK) et al. The results of this study provides information for further cloning and verifying the drought-resistant genes, digging new drought-related genes, understanding the molecular mechanism of drought-resistance, and breeding new varieties with high drought-resistance.
Skeletal Muscle Expression Characteristics of
IGF
-
1
Gene and Its SNPs Association with Growth Traits in Goat (
Capra hircus
)
LI Wen-Yang, LIU Yuan, WU Xian-Feng, HUANG Qin-Lou
2019, 27(12): 2188-2197 |
doi:
10.3969/j.issn.1674-7968.2019.12.010 | Full text
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Abstract
Major genes related to growth traits of goat (
Capra hircus
) were selected as marker assisted selection which can improve the accuracy of selection and accelerate breeding progress. The current study aimed to analyze gene expression characteristics of insulin-like growth factor-1 (
IGF
-
1
) gene in skeletal muscle, SNPs distribution and its association with growth traits of goats. qRT-PCR was used to analyze
IGF
-
1
gene expression level in masseter, trapezius, semispinalis, arm triceps, extensor carpi radialis longus, longissimus dorsi, psoas, quadriceps femoris, biceps femoris of Fuqing goat and Nubia black goat. PCR sequencing and high-resolution melting (HRM) technologies were carried out to screen SNPs and analyzed their association with growth trait in Fuqing goat (
n
=124), Nubia black goat (
n
=152), Jianyang big ear goat (
n
=121), Daiyun goat (
n
=20). The results revealed that
IGF
-
1
gene was expressed in 9 skeletal muscle tissues of Fuqing goat and Nubia black goat, and the expression level was different in skeletal muscle tissues and breeds. The expression level of
IGF
-
1
gene in 9 skeletal muscle tissues of Fuqing goat was lower than that of Nubia black goat. The expression level of
IGF
-
1
gene in masseter and quadriceps femoris was extremely significantly different between the 2 breeds (
P
<0.01), and the expression level of
IGF
-
1
gene in arm triceps and trapezius and longissimus dorsi was significantly different between the 2 breeds (
P
<0.05). The exon sequence of
IGF
-
1
gene was highly conserved, and no mutation was found in Fuqing goat and Nubia black goat. Most of the 3 SNPs of the 4 breeds showed moderate polymorphism distribution,
PIC
was 0.18~0.38; the 3 SNPs had obvious variety specificity on the growth traits of goats, and had significant influence on some growth traits of Jianyang big ear goat and Nubia black goat, but had little influence on the growth traits of Fuqing goat. The results of this study reveals the difference of
IGF
-
1
gene expression in the skeletal muscles of Fuqing goat and Nubia black goat, and provides basic data for further exploring the mechanism of goat growth and development. The research results unveile that 3 SNPs within
IGF
-
1
have strong effects on many growth traits of goats, which could be used as candidate markers for marker assisted selection of greater growth performance.
The Analysis on Genetic Evolution of Bian Chicken (
Gallus gallus
) Population Based on RAD-seq Technology
LI Guo-Hui, Wei Qing-Yu, ZHANG Hui-Yong, YIN Jian-Mei, XUE Qian, ZHU Yun-Fen, SU Yi-Jun, WANG Ke-Hua, ZOU Jian-Min, HAN Wei
2019, 27(12): 2198-2206 |
doi:
10.3969/j.issn.1674-7968.2019.12.011 | Full text
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Abstract
Bian chicken (
Gallus gallus
) is a valuable genetic resource as a Chinese native chicken. It is of great significance to explore the genetic diversity and molecular genetic evolution of the population at the molecular level. In this study, RAD-seq simplified genome sequencing technology was employed to identify SNP markers in Bian chickens and compare the genetic differences between the Bian chicken population and the other breeds population by calculating the genetic statistics. Functional annotation was conducted for the selected genes during evolution. The results showed that 319 727 SNP markers were identified in Bian chickens. The average observed heterozygosity (0.193) and nucleotide diversity (0.231) were in the medium levels, but inbreeding coefficient(0.167) was relatively high.The linkage disequilibrium analysis showed that there was no strong linkage disequilibrium between the alleles of Bian chickens population. The clustering results of the structure model showed that Bian chicken and Dagu chicken, Anyi gray chicken, Langshan chicken had a close relationship and belonged to the same type. 200 selected genes were identified through the
Fst
and
θπ
testing. Gene Ontology (GO) and KEGG analysis showed that these selected genes were mainly enriched in metabolism, neuroactive ligand-receptor interaction, mitogen-activated protein kinase (MAPK), vascular smooth muscle contraction signal pathways. The function analysis of the genes including nitric oxide synthase (
NOS2
), heterochromatin protein 1 binding protein 3 (
HP1BP3
), aprataxin (
APTX
), prostaglandin endoperoxide synthase 2 (
PTGS2
) and phospholipase A2 group 4 type alpha (
PLA2G4A
) was helpful to understand the molecular mechanism of special traits such as cold resistance, hypoxia, fertility, nervous system development and stress resistance in Bian chicken. The results of the study provide molecular basis for the genetic evolution and evaluation and conservation of local chicken breeds.
Expression Analysis of Antiviral Genes Related to BmNPV in Silkworm (
Bombyx mori
) and Screening of Practical Molecular Markers
LIU Yong AI, Jun-Wen, TANG Yun, XUE Hong, HE Xing-Jian, ZHENG Ying
2019, 27(12): 2207-2215 |
doi:
10.3969/j.issn.1674-7968.2019.12.012 | Full text
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Abstract
Bombyx mori nucleopolyhedrovirus
(BmNPV) is a highly pathogenic virus in the sericultural industry and often results in severe economic losses. Some proteins are found to show antiviral activity against BmNPV in previous studies, but little is known about the correlations between expression levels of these antiviral related genes and resistance abilities of different genetic materials against BmNPV. In this study, to explore the correlations, the highly resistant parent (R) was crossed with the highly susceptible parent (S) to generate different types of genetic materials such as F
1
, F
2
, and backcrosses. The resistance to BmNPV and the corresponding relative expression levels of 5 antiviral related genes including
Bmlipase
-
1
, serine protease Ⅱgene (
BmSP
-
2
), ribosomal protein S3A gene (
BmS3A
), suppressor of profilin 2 gene (
BmSop2
) and nicotinamide adenine dinucleotide phosphate oxidoreductase gene (
BmNOX
) in different genetic materials were detected by BmNPV attack test and fluorescent quantitative PCR (qRT-PCR) technology.The results showed that
BmSP
-
2
and
Bmlipase
-
1
specifically expressed in midgut, other genes showed no tissue specificity. The relative expression levels of 4 genes (
Bmlipase
-
1
,
BmSP
-
2
,
BmNOX
and
BmSop2
) were higher in midguts of different types of genetic materials with stronger viral resistance, which had significant differences in different types of genetic materials, being consistent with their resistance abilities. However, there was no correlation among the expression levels of
BmS3A
. The highest level of consistency between expression levels of these antiviral related genes and resistance abilities of different types of genetic materials against BmNPV had been observed in
Bmlipase
-1. It was concluded that relative expression levels of
Bmlipase
-1 could be one of the basis in selecting anti -BmNPV materials in silkworm breeding.
Functional Identification of
lin
-
41
Gene in
Heterorhabditidoides chongmingensis
LI Peng-Ya, HUANG Jin, ZHANG Ke-Yun
2019, 27(12): 2216-2226 |
doi:
10.3969/j.issn.1674-7968.2019.12.013 | Full text
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Abstract
Entomopathogenic nematodes (EPNs) are a class of highly effective and safety biocides whose capacity of reproduction is an important factor which affect the yield and quality of these EPNs as products potential. According to the differentially expression genes (DEGs) profile of the rabditid-EPN
Heterorhabditidoides chongmingensis
constructed in previous study, a RNA-binding protein lin-41 coding gene (
lin
-
41
) involved in regulating the development of nematodes was selected. The role of
lin
-
41
in the growth and development of
H. chongmingensis
was revealed by identifying the biological functions of this gene in the nematode. Conservative analysis results showed that the conserved region of
lin
-
41
of
H. chongmingensis
contained the non Hodgkin's lymphoma (NHL) superfamily domain and multiple NHL repeats. The amino acid sequences of lin-41 of
H
.
chongmingensis
,
Ancylostoma duodenale
,
Dictyocaulus viviparus
,
Caenorhabditis elegans
,
C. brenneri
and other related nematodes were highly conserved. The conserved NHL superfamily domain of the functional region fragment of
lin
-
41
was selected as interfering fragment, and then the double-stranded RNA (dsRNA) expression vector of the fragment was constructed by L4440 plasmid vector and transformed into
Escherichia?coli
HT115 (DE3). The expression of the target gene was disturbed in the
H. chongmingensis
by feeding with the transformed
E. coli
HT115 (DE3). The effects of RNAi on the expression level of
lin
-
41
and the reproductive related G protein α subunit gene (
goa
-
1
) were detected by qRT-PCR. The biological characteristics changes of the
H. chongmingensis
nematodes after
lin
-
41
RNAi were recorded. The relative expression of
lin
-
41
in
H. chongmingensis
after fed with the transformed
E. coli
HT115 (DE3) inducted by isopropyl-beta-D-thiogalactopyranoside (IPTG) with 0.1 mmoL/L for 4 h was reduced by 72.08% than that of the L4440 group. The number of eggs laid by the
lin
-
41
RANi group was significantly less than that of the L4440 group, with an average of 45 eggs reduced (
P
<0.05). However, there was no significant change in the hatching rate of eggs between the 2 groups. These results indicated that the decreased in the expression of
lin
-
41
neither affected the normal development and the hatch of eggs nor the quality of eggs. There were no significant change in body length between the 2 groups, although the female rate of the
lin
-
41
RNAi group was slightly higher than that of the control group. These results indicated that the reducing expression level of
lin
-
41
in
H. chongmingensi
neither affected the growth nor the sex differentiation of the nematode. In addition, RANi of
lin
-
41
significantly reduced the expression level of
goa
-
1
(
P
<0.05), which indicated that
lin
-
41
not only participated in the oogenesis of nematodes but also affected the spawning behavior of nematodes in the complex reproductive system of
H. chongmingensis
by influencing the expression level of other gene related to reproduction in nematodes. This result also suggested that the regulatory network of egg laying behaviors of
H. chongmingensi
including both
lin
-
41
and
goa
-
1
. The biological function of
lin
-
41
in
H. chongmingensis
was explored by RNAi method in present study, which involved in regulating the oogenesis of nematodes to affect the egg production of
H. chongmingensis
and in the egg laying behaviors of the nematode by regulating expression level of
goa
-
1
. This study provides important theoretical basis and technical support for the subsequent expansion, development and utilization of
H. chongmingensis
nematodes in agriculture.
Isolation, Identification, Physicochemical Parameters and Antibacterial Characteristics of
Byssochlamys
sp. from Shengzhou Nane (
Prunus salicina
var.
taoxingli
) Fruit
MO Yi-Wei, LIN Hai-Yan, ZHENG Meng-Qi, WANG Hai, YANG Guo, WANG Wei
2019, 27(12): 2227-2237 |
doi:
10.3969/j.issn.1674-7968.2019.12.014 | Full text
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Abstract
Shengzhou Nane (
Prunus salicina
var.
taoxingli
) usually ripe in mid-July, high temperatures and frequent rains accelerate water loss, softening, microbial attack and decay during storage. The aim of this study was to investigate and identify pathogens, reduce occurrence of diseases, and isolate and identify pathogenic bacteria as well as to detect the possible host. Initially, effects of light, temperature, pH and different C and N sources on colony growth was explored, and NaHCO
3
and chitosan oligosaccharide (COS) were used for antibacterial test. The results showed that the pathogen was
Byssochlamys
sp. (B-TXL-02), which can cause disease in a variety of fruits, including pear (
Pyrus
spp.), apple (
Malus domestica
), peach (
Prunus persica
), cherry (
Prunus avium
), apricot (
Prunus armeniaca
), grape (
Vitis vinifera
), mango (
Mangifera indica
), banana (
Musa
spp.) and others fruits, indicating that the host had broad spectrum. Continuous illumination inhibited colony growth. Optimal factors for
Byssochlamys
sp. growth were temperature 30 ℃, pH 5, D-fructose and glucose for C source, beef extract and yeast extract for N source. When added into the potato dextrose agar, NaHCO
3
and COS could significantly inhibit colony growth in the first 6 d and the first 12 d, respectively, by inhibiting spore germination and inhibited mycelial growth. Treated with 0.3% NaHCO
3
+1.6% chitosan oligosaccharide, the postharvest rot rate of fruit was significantly reduced. This study provides a practical method for prevention and control of
Byssochlamys
sp. for Shengzhou Nane during postharvest storage.
Screening of Antagonistic Bacteria Against
Fusarium
Wilt of Watermelon (
Citrullus lanatus
) and Its Antagonistic Properties
XU Wei-Hui, WANG Heng-Xu, ZHAO Jing-Ming, WANG Zhi-Gang, WANG Ke-Xin
2019, 27(12): 2238-2247 |
doi:
10.3969/j.issn.1674-7968.2019.12.015 | Full text
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Abstract
Fusarium
wilt of watermelon (
Citrullus lanatus
) is caused by
Fusarium oxysporum
f.sp.
niveum
(FON) which is considered as the most important soil-borne pathogens. Some safe antagonistic strain can control FON growth and reduce
Fusarium
wilt of watermelon. In order to screen an antagonistic strain against FON, the rhizosphere soil from vegetable crops on Qinxin farm in Qiqihar Heilongjiang province was collected and used in this study. The antagonistic strain was screened out using plate confrontation method, and identified by morphological, physiological, and biochemical and bio-control enzyme analyses, as well as
16S
rDNA sequence analysis. Antifungal activities of sterile fermentation filtrate from different growth stage of antagonistic strain and the stability of sterile fermentation filtrate under different conditions were determined using growth rate method. FON spore morphology and cell membrane integrity were analyzed by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The results showed that the antagonistic strain was classified as
Bacillus methylotrophicus
, named as WC. The WC strain could product amylase, glucanase, protease and siderophores. The sterile fermentation filtrate from the stationary phase had stronger antifungal activity against FON compared to those from the exponential stage and death phase, and the inhibition rate of FON colony growth was 61.57%. The stability tests showed that the sterile fermentation filtrate had stronger antifungal activity against FON under 10 ℃ for 30 min compared to other testing temperature, with inhibition rate of 62.78%. The antifungal activity from WC fermentation filtrate reached to 74.54% in pH 7, the stabilities of fermentation filtrate were poor in acid and base conditions. The filtrate could be stored with stable antifungal activity at 4 ℃ for 30 d and was insensitive to UV-irradiation. The analyses from SEM demonstrated that treatment with fermentation filtrate from WC led to wrinkling and depressed changes on the surface of FON spores. The CLSM revealed that the fermentation filtrate from WC damaged membrane integrity. The above results indicate that WC is a high-efficiency antagonistic strain against FON, and could be used to control
Fusarium
wilt of watermelon in future.
Identification of a Tobacco (
Nicotiana tobacum
) PGPR Strain and Optimization for Its Fermentation Conditions by Response Surface Analysis Method
WU Xiang, XIE Li-Yuan, TAN Hao, GAN Bing-Cheng, PENG Wei-Hong, HUANG Zhong-Qian
2019, 27(12): 2248-2257 |
doi:
10.3969/j.issn.1674-7968.2019.12.016 | Full text
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Abstract
The definite taxonomic classification and fermentation conditions of the functional bacterial could be more efficient for biofertilizer development. Plant growth-promoting rhizobacteria (PGPR) strain MT-002-B-12 is promising isolate for tobacco biofertilizer production as a potential supplementary microbe. The aim of this study is to identify its taxonomic classification, and further optimize the conditions in fermentation. The phylogeny of PGPR strain MT-002-B-12 was analyzed by phenotypic features, physiological-biochemical characteristics and
16S
rDNA gene sequence alignments. The fermentation conditions of MT-002-B-12 to produce indole-3-acetic acid (IAA) were optimized by combining the single factor condition analysis and response surface analysis method. The result of classification showed that MT-002-B-12 was
Klebsiella variicola
. The fermentation experiments showed that the optimum fermentation conditions for MT-002-B-12 was culture volume 30% (V/V), initial pH 6.0, temperature 25 ℃, shaker speed 150 r/min, culture time 34 h; and the optimum content of nutrients in the medium was 1.11% sucrose, 1.36% peptone, 0.15‰ MgSO
4
·7H
2
O, 0.34‰ CaCl
2
·2H
2
O. The strain MT-002-B-12 enriched the species of growth promoting bacteria, and could be used as a strain resource for the development of tobacco biofertilizer.
Reviews and Progress
MEN1
/Menin Regulates the Pathogenesis of Non-Alcoholic Fatty Liver Disease
LI Ran-Ran, XU Zhong-Jin, WANG Sheng-Xuan, YAN Chuan, SI Bo, ZHANG Le-Tian, ZHANG Xuan, LIU Ting-Jun, SHI Ke-Rong
2019, 27(12): 2258-2264 |
doi:
10.3969/j.issn.1674-7968.2019.12.017 | Full text
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Abstract
Nonalcoholic fatty liver disease (NAFLD) is a clinical pathological syndrome characterized by hepatic steatosis and lipid storage. It is caused by fatty acid synthesis, oxidation, transport, insulin resistance, oxidative stress, gluconeogenesis and other aspects. It was found that the protein menin encoded by the tumor suppressor gene
MEN1
can be widely involved in pathways that regulating the liver metabolism.
MEN1
/menin was an important regulator of liver metabolism and assumed to be closely associated with the pathogenesis of fatty liver disease. This article generally elucidate the research progress of menin in regulating the lipid metabolism, glucose metabolism, insulin resistance and also inflammation.
Functional Nucleic Acid-based Biosensing Technique for Genetically Modified Ingredients Detection
DUAN Xing-Yang, TIAN Jing-Jing, ZHANG Yuan, SHANG Ying, HUANG Kun-Lun, XU Wen-Tao
2019, 27(12): 2265-2271 |
doi:
10.3969/j.issn.1674-7968.2019.12.018 | Full text
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Abstract
The transgenic technology has been concerned greatly by people all over the world nowadays. Genetically modified organisms (GMOs),especially the GM crops have caused several controversial issues, including health problems, ecological environmental risks and even ethical concerns. From the perspective of 'Functional Nucleic Acid' and 'Biosensors', this review summarized molecular amplification techniques, different ways of signal output and nanomaterials -based functional nucleic acid biosensors for detection of genetically modified ingredients. Finally, the challenges and trends in the future development of genetically modified components' detection are prospected. This review will be helpful for promoting the development of test techniques for GMOs and the progress of functional nucleic acid-based biosening disciplines.
Popularization and Application
New Germplasm of Meishan Pig (
Sus scrofa
) with High Lean-meat Rate was Created by Editing Pig
MSTN
Gene with ZFN Technique
CUI Wen-Tao, XIE Shan-Shan, LI Xiang, BI Han-Fang
2019, 27(12): 2272-2280 |
doi:
10.3969/j.issn.1674-7968.2019.12.019 | Full text
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Abstract
Myostatin (MSTN) is an important negative regulator of muscle development. Mutations of
MSTN
gene can lead to muscle hypertrophy in many natural species. However, there was not been reported significant muscle phenotype in pigs (
Sus scrofa
) in association with
MSTN
mutation. Researchers from Institute of Animal Sciences, Chinese Academy of Agricultural Sciences used zinc-finger nucleases (ZFN) editing technique in combination with somatic cell nuclear transfer and embryo transfer techniques to knock out the
MSTN
gene of Meishan pig's fetal fibroblast, and obtained the first
MSTN
gene editing Meishan pigs in the world. The homozygous
MSTN
mutation (
MSTN
-/-
) Meishan pigs had a distinct double-muscle phenotype with broad back, full hips and well-developed front shoulders. The lean-meat rate could reach more than 60%, which was nearly 20% higher than wild type. It had reached the same level as exotic pig breeds, effectively solving the technical bottleneck that restricted the development of local black pigs in China. The gene editing pig had not any marker gene or any integrated carrier fragment in the genome, and there was no off-target phenomenon. It was more reliable in animal health and product safety. Additionally, it had been approved by the Ministry of Agriculture to enter the stage of production test safety evaluation. The patent for the preparation of the related achievements and the patent for the protection of
MSTN
mutant sequences had been granted by the National Invention Patents. At present, this achievement has good industrialization prospects in terms of safety and breeding value, which could bring enormous economic benefits to the society.
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