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Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice
ZHANG Xi-juan, LAI Yong-cai, MENG Ying, TANG Ao, DONG Wen-jun, LIU You-hong, LIU Kai, WANG Li-zhi, YANG Xian-li, WANG Wen-long, DING Guo-hua, JIANG Hui, REN Yang, JIANG Shu-kun
2023, 22 (2): 325-340.   DOI: 10.1016/j.jia.2022.08.080
Abstract599)      PDF in ScienceDirect      

Rice direct seeding has the significant potential to save labor and water, conserve environmental resources, and reduce greenhouse gas emissions tremendously.  Therefore, rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.  Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice (DSR) production.  This study used a permanent mapping population with 144 recombinant inbred lines (RILs) and 2 828 bin-markers to detect quantitative trait loci (QTLs) associated with mesocotyl length in 2019 and 2020.  The mesocotyl lengths of the rice RILs and their parents, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), were measured in a growth chamber at 30°C in a dark environment.  A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2), 2(4), 3(2), 4, 5, 6, 7, 9, 11(2), and 12.  Seven of these QTLs, including qML1a, qML1b, qML2d, qML3a, qML3b, qML5, and qML11b, were reproducibly detected in both years via the interval mapping method.  The major QTL, qML3a, was reidentified in two years via the composite interval mapping method.  A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb, respectively.  Thirteen predicted genes within a relatively small genetic interval (88.18 kb) of the major mesocotyl elongation QTL, qML3a, were more thoroughly analyzed.  Finally, the coding DNA sequence variations among SN265, LTH, and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.  This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.  Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.  In conclusion, these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.  This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development.

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Interaction of soil microbial communities and phosphorus fractions under long-term fertilization in paddy soil 
Muhammad QASWAR, Waqas AHMED, HUANG Jing, LIU Kai-lou, ZHANG Lu, HAN Tian-fu, DU Jiang-xue, Sehrish ALI, Hafeez UR-RAHIM, HUANG Qing-hai, ZHANG Hui-min
2022, 21 (7): 2134-2144.   DOI: 10.1016/S2095-3119(21)63733-4
Abstract132)      PDF in ScienceDirect      
Understanding the impact of biological activities on the soil phosphorus (P) distribution under long-term fertilizer application can facilitate better soil P fertility management.  Therefore, the primary objectives of this study were to investigate the effect of long-term (since 1981) fertilizer application on the soil P fractions and microbial community and to evaluate correlations between the microbial community structure and P distribution.  The following treatments were implemented in a long-term field trial: no fertilization (CK), inorganic N and K (NK), inorganic P and K (PK), inorganic N, P and K (NPK) and manure+NPK (MNPK) fertilization.  The study showed that the soil pH, soil organic carbon and total and available N and P concentrations were considerably higher in the MNPK treatment than in the CK treatment.  The soil microbial biomass C, N and P concentrations were also significantly higher in the MNPK treatment than in the CK treatment.  Among fertilization treatments, the β-1,4-glucosidase, α-1,4-glucosidase, urease, acid phosphatase and phosphodiesterase activities were the highest in the MNPK treatment.  Compared to inorganic fertilization, the MNPK treatment increased the labile soil P fractions and decreased the residual soil P concentration.  Continuous fertilization significantly affected the soil microbial composition.  The total phospholipid fatty acid (PLFA) concentrations in the NK, PK, NPK and MNPK treatments were 23.3, 43.1, 48.7 and 87.7% higher, respectively, than in the CK treatment.  A significant correlation was observed between the microbial community and soil P fractions.  Moreover, the aggregated boosted tree (ABT) model showed that among the various soil biochemical properties, the total PLFA concentration was the factor that most influenced the active P pool, accounting for 35.4% of the relative influence of all soil biochemical properties examined.  These findings reveal that combined manure and inorganic fertilizer application is a better approach than applying inorganic fertilizer alone for sustaining long-term P fertility by mediating soil biological activity.


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Susceptibility and tissue specificity of Spodoptera frugiperda to Junonia coenia densovirus
CHEN Zu-wen, YANG Yan-chao, ZHANG Jian-feng, JIN Ming-hui, XIAO Yu-tao, XIA Zhi-chao, LIU Yuan-yuan, YU Sai-zhen, YANG Yong-bo, WANG Yuan, LI Yi, LIU Kai-yu
2021, 20 (3): 840-849.   DOI: 10.1016/S2095-3119(20)63163-X
Abstract113)      PDF in ScienceDirect      
The fall armyworm, Spodoptera frugiperda, which destroys many economic crops such as rice and maize, has recently invaded China.  Insect viruses as biological control agents play important roles in killing pests.  One potential viral insecticide is the environmentally highly infective and virulent densovirus.  We successfully rescued Junonia coenia densovirus (JcDV) using its infectious clone in different insect cell lines and larvae of three insect species.  Results showed that the lysate of cultured insect cells transfected by the JcDV infectious clone killed the 2nd instar S. frugiperda.  The LD50 of homogenate from JcDV-infected Spodoptera litura to the 2nd instar S. frugiperda (1.76×108 viral genome copies per larva during 10 d post infection) was higher than that of the 2nd instar S. litura (7.39×107 JcDV genome copies) or Helicoverpa armigera larvae (9.71×107 JcDV genome copies).  The LT50 of the S. litura homogenate (2.60×109 viral genome copies each larva) to the 2nd instar S. frugiperda was 6.96 d, longer than that of the S. litura (6.18 d) or the 2nd instar H. armigera (5.94 d).  JcDV could infect the fat body of H. armigera, but not S. frugiperda or S. litura.  Although JcDV can infect all three lepidopteran species, their susceptibility to the virus differs.  JcDV has great potential as a biological control agent against pests such as S. frugiperda.
 
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Comparative analysis of the ecological fitness and transcriptome between two genotypes of the brown planthopper Nilaparvata lugens
LIU Kai, CHEN Zhan, SU Qin, YUE Lei, CHEN Wei-wen, ZHANG Wen-qing
2020, 19 (6): 1501-1511.   DOI: 10.1016/S2095-3119(19)62768-1
Abstract119)      PDF in ScienceDirect      
Insect quantity is an important index for determining the degree of damage to plants.  The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most important rice pests in Asia.  Here, we used two genotypes of BPH, a high-fecundity genotype (HFG) and a low-fecundity genotype (LFG), to measure their ecological fitness and to explore possible causes for genotype differentiation by transcriptome sequencing.  Our results showed that there were significant differences in body weight, egg hatching rate and honeydew secretion between the HFG and LFG, particularly, the number of eggs laid per female was more significant.  Transcriptional analysis showed that a total of 1 966 differentially expressed genes (DEGs) were mainly involved in energy metabolism, carbohydrate and lipid synthesis, insect hormone synthesis and fecundity-related pathways.  Moreover, we found that the phosphorylation levels of AMPK, AKT and FoxO and the synthesis of ecdysone were different between the two genotypes of BPH.  These findings may partially explain the difference in the ecological fitness between HFG and LFG.  This study is the first to compare the differences between two genotypes of BPH and to provide transcriptomic evidence to further understand the fecundity of BPH.
 
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Change of soil productivity in three different soils after long-term field fertilization treatments
LIU Kai-lou, HAN Tian-fu, HUANG Jing, ZHANG Shui-qing, GAO Hong-jun, ZHANG Lu, Asad SHAH, HUANG Shao-min, ZHU Ping, GAO Su-duan, MA Chang-bao, XUE Yan-dong, ZHANG Hui-min
2020, 19 (3): 848-858.   DOI: 10.1016/S2095-3119(19)62742-5
Abstract116)      PDF in ScienceDirect      
Soil productivity (SP) without external fertilization influence is an important indicator for the capacity of a soil to support crop yield. However, there have been difficulties in estimating values of SPs for soils after various long-term field treatments because the treatment without external fertilization is used but is depleted in soil nutrients, leading to erroneous estimation. The objectives of this study were to estimate the change of SP across different cropping seasons using pot experiments, and to evaluate the steady SP value (which is defined by the basal contribution of soil itself to crop yield) after various longterm fertilization treatments in soils at different geographical locations. The pot experiments were conducted in Jinxian of Jiangxi Province with paddy soil, Zhengzhou of Henan Province with fluvo-aquic soil, and Gongzhuling of Jilin Province with black soils, China. Soils were collected after long-term field fertilization treatments of no fertilizer (control; CK-F), chemical fertilizer (NPK-F), and combined chemical fertilizer with manure (NPKM-F). The soils received either no fertilizer (F0) or chemical fertilizer (F1) for 3–6 cropping seasons in pots, which include CK-P (control; no fertilizer from long-term field experiments for pot experiments), NPK-P (chemical fertilizer from long-term field experiments for pot experiments), and NPKM-P (combined chemical and organic fertilizers from long-term field experiments for pot experiments). The yield data were used to calculate SP values. The initial SP values were high, but decreased rapidly until a relatively steady SP was achieved at or after about three cropping seasons for paddy and fluvo-aquic soils. The steady SP values in the third cropping season from CK-P, NPK-P, and NPKM-P treatments were 37.7, 44.1, and 50.0% in the paddy soil, 34.2, 38.1, and 50.0% in the fluvo-aquic soil, with the highest value observed in the NPKM-P treatment for all soils. However, further research is required in the black soils to incorporate more than three cropping seasons. The partial least squares path mode (PLS-PM) showed that total N (nitrogen) and C/N ratio (the ratio of soil organic carbon and total N) had positive effects on the steady SP for all three soils. These findings confirm the significance of the incorporation of manure for attaining high soil productivity. Regulation of the soil C/N ratio was the other main factor for steady SP through fertilization management.
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Comparison of carbon sequestration efficiency in soil aggregates between upland and paddy soils in a red soil region of China
LIU Kai-lou, HUANG Jing, LI Da-ming, YU Xi-chu, YE Hui-cai, HU Hui-wen, HU Zhi-hua, HUANG Qing-hai, ZHANG Hui-min
2019, 18 (6): 1348-1359.   DOI: 10.1016/S2095-3119(18)62076-3
Abstract221)      PDF in ScienceDirect      
There is limited information on carbon sequestration efficiency (CSE) of soil aggregates in upland and paddy soils under long-term fertilization regimes.  In a red soil region of southern China, an upland soil experiment started in 1986 and a paddy soil experiment commenced in 1981.  These experiments were conducted using different fertilization treatments.  After 30 years, soil organic carbon (SOC) content and stock of different aggregate components were analyzed.  The results showed that the SOC contents and stocks in upland soil were lower than in paddy soil.  In both upland and paddy soils, the SOC contents and stocks of all aggregate components in NPKM (combined treatment with chemical nitrogen (N), phosphorus (P), potassium (K) fertilizers and manure) were the highest among all treatments.  Compared with CK (no fertilizer), SOC content of all aggregate components in NPKM was increased by 13.21–63.11% and 19.13–73.33% in upland and paddy soils, respectively.  Meanwhile, the change rates in SOC stock of all aggregate components in upland soil were lower than in paddy soil, although the change rate of SOC stock of all aggregate components in NPKM was higher than in other treatments.  Furthermore, a linear equation could fit the relationships between carbon (C) input and change rate of SOC stock (P<0.05).  Results indicated that the sum of CSE from all aggregate components in upland soil (16.02%) was higher than that of paddy soil (15.12%) in the same climatic condition and from the same parent material.  However, the CSEs from all aggregates were higher than that of bulk soil, although the result from bulk soil also showed that the CSE of upland soil was higher than that of paddy soil.
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Effects of sesame nectar on longevity and fecundity of seven Lepidoptera and survival of four parasitoid species commonly found in agricultural ecosystems
LIU Kai, ZHU Ping-yang, Lü Zhong-xian, CHEN Gui-hua, ZHANG Jing-ming, Lü Yao-bing, LU Yan-hui
2017, 16 (11): 2534-2546.   DOI: 10.1016/S2095-3119(17)61665-4
Abstract699)      PDF in ScienceDirect      
Ecological engineering involves the use of plants to promote establishment, survival and efficiency of natural enemies in agricultural systems.  Some plant species may be hosts or provide resources to some pest species.  We assessed the risks and benefits of sesame (Sesamum indicum L.), as a nectar source for seven economically important Lepidopteran pest and four parasitoid species in a range of vegetable crop systems.  Our results showed that the mean longevities of arthropod parasitoids Pteromalus puparum (L.), Encarsia sophia (Girault & Dodd) and male Microplitis tuberculifer (Wesmael) were significantly extended when fed on sesame flowers compared to the water control.  Sesame flowers had no effect on adult longevities and fecundities of six out of the seven Lepidoptera pest species tested except Plutella xyllostella (L.) females laid more eggs when fed on sesame flowers.  It is likely that the increased fecundity is due to accessibility to nectar at the bottom of corolla because of their smaller body sizes.  Our findings provide a first step towards better understanding of the risks and benefits of using sesame to implement ecological engineering for the management of vegetable pests.
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Electrophysiological responses of the rice striped stem borer Chilo suppressalis to volatiles of the trap plant vetiver grass (Vetiveria zizanioides L.)
LU Yan-hui, LIU Kai, ZHENG Xu-song, LÜ Zhong-xian
2017, 16 (11): 2525-2533.   DOI: 10.1016/S2095-3119(17)61658-7
Abstract715)      PDF in ScienceDirect      
Vetiver grass (Vetiveria zizanioides L.) was previously found to effectively attract female adults of Chilo suppressalis (Walker), an important pest of rice.  To determine the volatile compounds involved in this attraction, electroantennography (EAG) responses to seven synthetic volatiles released from vetiver plants were examined.  Our results indicated that the responses of C. suppressalis adult antennae to the different compounds varied widely.  The compounds elicited strong EAG responses in female antennae were subsequently selected for further EAG response tests, namely, caryophyllene, β-ocimene, linalool and α-pinene.   EAG responses to a combination of these four compounds did not differ significantly from the individual compounds.  However, pair combination tests indicated that 0.01 μg μL–1 linalool and 50 μg μL–1 α-pinene, 50 μg μL–1 caryophyllene and 0.01 μg μL–1 linalool, 0.01 μg μL–1 β-ocimene and 0.01 μg μL–1 linalool, and 0.01 μg μL–1 β-ocimene and 50 μg μL–1 caryophyllene elicited significantly greater EAG responses in 3-day female moths compared to the 1-day female.  These compound combinations and the corresponding ratios are probably playing an important role in attracting female adults of C. suppressalis to the vetiver grass.  
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Conditional and unconditional QTLs mapping of gluten strength in common wheat (Triticum aestivum L.)
LIU Tong-tong, LIU Kai, WANG Fang-fang, ZHANG Ying, LI Qing-fang, ZHANG Kai-ran, XIE Chu-peng, TIAN Ji-chun, CHEN Jian-sheng
2017, 16 (10): 2145-2155.   DOI: 10.1016/S2095-3119(16)61564-2
Abstract707)      PDF in ScienceDirect      
    Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantitative trait loci (QTLs) analysis for gluten strength, as measured by sedimentation volume (SV) and gluten index (GI), was performed using the QTLNetwork 2.0 software. Recombinant inbred lines (RILs) derived from the winter wheat varieties Shannong 01-35×Gaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identified using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15–45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals: WPT-3743–GLU-D1 (1D), WPT-7001–WMC258 (1B), and WPT-8682–WPT-5562 (1B). Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs (QGi1D-13 and QSv1D-14) and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.
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Effects of Long-Term Organic Amendments on Soil Organic Carbon in a Paddy Field: A Case Study on Red Soil
HUANG Qing-hai, LI Da-ming, LIU Kai-lou, YU Xi-chu, YE Hui-cai, HU Hui-wen, XU Xiao-lin
2014, 13 (3): 570-576.   DOI: 10.1016/S2095-3119(13)60714-5
Abstract1759)      PDF in ScienceDirect      
Soil organic carbon (SOC) is one of the main carbon reservoirs in the terrestrial ecosystem. It is important to study SOC dynamics and effects of organic carbon amendments in paddy fields because of their vest expansion in south China. A study was carried out to evaluate the relationship between the SOC content and organic carbon input under various organic amendments at a long-term fertilization experiment that was established on a red soil under a double rice cropping system in 1981. The treatments included non-fertilization (CK), nitrogen-phosphorus-potassium fertilization in early rice only (NPK), green manure (Astragalus sinicus L.) in early rice only (OM1), high rate of green manure in early rice only (OM2), combined green manure in early rice and farmyard manure in late rice (OM3), combined green manure in early rice, farmyard manure in late rice and rice straw mulching in winter (OM4), combined green manure in early rice and rice straw mulching in winter (OM5). Our data showed that the SOC content was the highest under OM3 and OM4, followed by OM1, OM2 and OM5, then NPK fertilization, and the lowest under non-fertilization. However, our analyses in SOC stock indicated a significant difference between OM3 (33.9 t ha-1) and OM4 (31.8 t ha-1), but no difference between NPK fertilization (27 t ha-1) and nonfertilization (28.1 t ha-1). There was a significant linear increase in SOC over time for all treatments, and the slop of linear equation was greater in organic manure treatments (0.276-0.344 g kg-1 yr-1) than in chemical fertilizer (0.216 g kg-1 yr-1) and no fertilizer (0.127 g kg-1 yr-1).
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