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Comparative transcriptome and lipidome reveal that a low K+ signal effectively alleviates the effect induced by Ca2+ deficiency in cotton fibers
GUO Kai, GAO Wei, ZHANG Tao-rui, WANG Zu-ying, SUN Xiao-ting, YANG Peng, LONG Lu, LIU Xue-ying, WANG Wen-wen, TENG Zhong-hua, LIU Da-jun, LIU De-xin, TU Li-li, ZHANG Zheng-sheng
2023, 22 (8): 2306-2322.   DOI: 10.1016/j.jia.2023.01.002
Abstract194)      PDF in ScienceDirect      
Calcium (Ca2+) plays an important role in determining plant growth and development because it maintains cell wall and
membrane integrity. Therefore, understanding the role of Ca2+ in carbon and lipid metabolism could provide insights
into the dynamic changes in cell membranes and cell walls during the rapid elongation of cotton fibers. In the present
study, we found that the lack of Ca2+ promoted fiber elongation and rapid ovule expansion, but it also caused tissue
browning in the ovule culture system. RNA-sequencing revealed that Ca2+ deficiency induced cells to be highly oxidized,
and the expression of genes related to carbon metabolism and lipid metabolism was activated significantly. All gene
members of nine key enzymes involved in glycolysis were up-regulated, and glucose was significantly reduced in Ca2+
deficiency-treated tissues. Ca2+ deficiency adjusted the flowing of glycolysis metabolic. However, low K+ recovered
the expression levels of glycolysis genes and glucose content caused by Ca2+ deficiency. Electrospray ionizationtandem
mass spectrometry technology was applied to uncover the dynamic profile of lipidome under Ca2+ and K+
interacted conditions. Ca2+ deficiency led to the decrease of fatty acid (FA), diacylglycerol (DAG), glycolipid and the
significant increase of triacylglycerol (TAG), phospholipid phosphatidylethanolamine (PE), phosphatidylglycerol (PG),
and PC (phosphatidylcholine). Low K+ restored the contents of FA, phospholipids, and glycolipids, effectively relieved
the symptoms caused by Ca2+ deficiency, and recovered the development of fiber cells. This study revealed dynamic
changes in transcript and metabolic levels and uncovered the signaling interaction of Ca2+ deficiency and low K+ in
glycolysis and lipid metabolism during fiber development.
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Millet/peanut intercropping at a moderate N rate increases crop productivity and N use efficiency, as well as economic benefits, under rain-fed conditions
LIU Zhu, NAN Zhen-wu, LIN Song-ming, YU Hai-qiu, XIE Li-yong, MENG Wei-wei, ZHANG Zheng, WAN Shu-bo
2023, 22 (3): 738-751.   DOI: 10.1016/j.jia.2022.08.078
Abstract298)      PDF in ScienceDirect      

Cereal and legume intercropping has been widely adopted to increase crop productivity in sustainable farming systems worldwide.  Among different intercropping combinations, millet and peanut intercropping can be adapted to most water-limited areas.  However, there are few studies on the differences in yield characteristics and nitrogen use efficiency between millet/peanut intercropping and monocultures under different nitrogen (N) application rates.  The objective of this study was to determine the yield advantages and economic benefits, as well as the appropriate N application rate, of millet/peanut intercropping.  A two-year field experiment was conducted with three cropping patterns (monoculture millet, monoculture peanut and millet/peanut intercropping) and four N rates (0, 75, 150 and 225 kg ha−1).  The results showed that the land equivalent ratio (LER) and net effect (NE) of the intercropping system reached their highest levels at the N input of 150 kg ha−1 in 2018 and 2019 (1.04 for LER, 0.347 Mg ha−1 for NE, averaged across two years).  Millet was the dominant crop in the intercropping system (aggressivity of millet and peanut (Amp)>0, competitive ratio of millet and peanut (CRmp)>1), and millet yields achieved their highest values at N inputs of 225 kg ha−1 for monoculture and 150 kg ha−1 for intercropping.  NUE reached its highest levels with N inputs of 150 kg ha−1 for all planting patterns over the two years.  Intercropping combined with an N input of 150 kg ha−1 achieved the highest net income of 2 791 USD ha−1, with a benefit-cost ratio of 1.56, averaged over the two years.  From the perspective of economics and agricultural sustainable development, millet/peanut intercropping at 150 kg N ha−1 seems to be a promising alternative to millet or peanut monoculture.

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Occurrence pattern and morphological polymorphism of weedy rice in China
WANG Hao-quan, DAI Wei-min, ZHANG Zi-xu, LI Meng-shuo, MENG Ling-chao, ZHANG Zheng, LU Huan, SONG Xiao-ling, QIANG Sheng
2023, 22 (1): 149-169.   DOI: 10.1016/j.jia.2022.08.001
Abstract303)      PDF in ScienceDirect      
Rice, the main food crop in China, has been sporadically reported to suffer from weedy rice infestation.  However, the overall occurrence and distribution pattern of Chinese weedy rice remains unclear because a systematic survey has not been conducted.  In order to reveal the infestation of Chinese weedy rice, a field survey was conducted in 999 sampling sites all over the rice-growing regions in China from 2009 to 2016 using seven-scale visual scoring of the level of weed infestation.  Weedy rice was found 39% occurrence incidence in a total of 387 sites.  The sampling sites with 50% or higher overall weedy rice infestation index mainly radiated from Jiangsu, Heilongjiang, Ningxia and Guangdong to the whole East China, Northeast China, Northwest China and South China.  A total of 45 morphological characters from 287 populations (collected simultaneously with the field survey) out of those occurred sites were observed and analyzed using multivariate analysis in common gardens with the same cultivation conditions in 2017 and 2019.  Canonical correlation analysis showed that 45 morphological characters were significantly related to the latitude, mean temperature, minimum temperature, precipitation and mean diurnal range factors.  The 287 weedy rice populations were divided into three morphological groups with climate-dependent geographical differentiation: strong tiller type only in Jiangsu, large leaf type in South China and Central China and large grain type mainly in North China.  Weedy rice seriously infested rice fields and had a geography, climate and cultivated rice type-dependent morphological and biotype differentiation in China.  It is suggested to pay attention to the harmfulness of weedy rice and adopt comprehensive control strategies.
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The water-saving potential of using micro-sprinkling irrigation for winter wheat production on the North China Plain
ZHAI Li-chao, Lü Li-hua, DONG Zhi-qiang, ZHANG Li-hua, ZHANG Jing-ting, JIA Xiu-ling, ZHANG Zheng-bin
2021, 20 (6): 1687-1700.   DOI: 10.1016/S2095-3119(20)63326-3
Abstract175)      PDF in ScienceDirect      
The shortage of groundwater resources is a considerable challenge for winter wheat production on the North China Plain.  Water-saving technologies and procedures are thus urgently required.  To determine the water-saving potential of using micro-sprinkling irrigation (MSI) for winter wheat production, field experiments were conducted from 2012 to 2015.  Compared to traditional flooding irrigation (TFI), micro-sprinkling thrice with 90 mm water (MSI1) and micro-sprinkling four times with 120 mm water (MSI2) increased the water use efficiency by 22.5 and 16.2%, respectively, while reducing evapotranspiration by 17.6 and 10.8%.  Regardless of the rainfall pattern, MSI (i.e., MSI1 or MSI2) either stabilized or significantly increased the grain yield, while reducing irrigation water volumes by 20–40%, compared to TFI.  Applying the same volumes of irrigation water, MSI (i.e., MSI3, micro-sprinkling five times with 150 mm water) increased the grain yield and water use efficiency of winter wheat by 4.6 and 11.7%, respectively, compared to TFI.  Because MSI could supply irrigation water more frequently in smaller amounts each time, it reduced soil layer compaction, and may have also resulted in a soil water deficit that promoted the spread of roots into the deep soil layer, which is beneficial to photosynthetic production in the critical period.  In conclusion, MSI1 or MSI2 either stabilized or significantly increased grain yield while reducing irrigation water volumes by 20–40% compared to TFI, and should provide water-saving technological support in winter wheat production for smallholders on the North China Plain.
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Effects of deep vertical rotary tillage on the grain yield and resource use efficiency of winter wheat in the Huang-Huai-Hai Plain of China
WU Fen, ZHAI Li-chao, XU Ping, ZHANG Zheng-bin, Elamin Hafiz BAILLO, Lemessa Negasa TOLOSA, Roy Njoroge KIMOTHO, JIA Xiu-ling, GUO Hai-qian
2021, 20 (2): 593-605.   DOI: 10.1016/S2095-3119(20)63405-0
Abstract130)      PDF in ScienceDirect      
Tillage represents an important practice that is used to dynamically regulate soil properties, and affects the grain production process and resource use efficiency of crops. The objectives of this 3-year field study carried out in the Huang-Huai-Hai (HHH) Plain of China were to compare the effects of a new deep vertical rotary tillage (DVRT) with the conventional shallow rotary tillage (CT) on soil properties, winter wheat (Triticum aestivum L.) grain yield and water and nitrogen use efficiency at different productivity levels, and to identify a comprehensive management that optimizes both grain yield and resource use efficiency in the HHH Plain. A split-plot design was adopted in field experiments in the winter wheat growing seasons of 2016–2017 (S1), 2017–2018 (S2) and 2018–2019 (S3), with DVRT (conducted once in June 2016) and CT performed in the main plots. Subplots were treated with one of four targeted productivity level treatments (SH, the super high productivity level; HH, the high productivity and high efficiency productivity level; FP, the farmer productivity level; ISP, the inherent soil productivity level). The results showed that the soil bulk density was reduced and the soil water content at the anthesis stage was increased in all three years, which were due to the significant effects of DVRT. Compared with CT, grain yields, partial factor productivity of nitrogen (PFPN), and water use efficiency (WUE) under DVRT were increased by 22.0, 14.5 and 19.0%. Path analysis and direct correlation decomposition uncovered that grain yield variation of winter wheat was mostly contributed by the spike numbers per area under different tillage modes. General line model analysis revealed that tillage mode played a significant role on grain yield, PFPN and WUE not only as a single factor, but also along with other factors (year and productivity level) in interaction manners. In addition, PFPN and WUE were the highest in HH under DVRT in all three growth seasons. These results provided a theoretical basis and technical support for coordinating the high yield with high resource use efficiency of winter wheat in the resource-restricted region in the HHH Plain of China.
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Differentially expressed miRNAs in anthers may contribute to the fertility of a novel Brassica napus genic male sterile line CN12A
Dong Yun, Wang Yi, Jin Feng-wei, Xing Li-juan, Fang Yan, Zhang Zheng-ying, ZOU Jun-jie, Wang Lei, Xu Miao-yun
2020, 19 (7): 1731-1742.   DOI: 10.1016/S2095-3119(19)62780-2
Abstract95)      PDF in ScienceDirect      
In Brassica napus L. (rapeseed), complete genic male sterility (GMS) plays an important role in the utilization of heterosis.  Although microRNAs (miRNAs) play essential regulatory roles during bud development, knowledge of how GMS is regulated by miRNAs in rapeseed is rather limited.  In this study, we obtained a novel recessive GMS system, CN12AB.  The sterile line CN12A has defects in tapetal differentiation and degradation.  Illumina sequencing was employed to examine the expression of miRNAs in the buds of CN12A and the fertile line CN12B.  We identified 85 known miRNAs and 120 novel miRNAs that were expressed during rapeseed anther development.  When comparing the expression levels of miRNAs between CN12A and CN12B, 19 and 18 known miRNAs were found to be differentially expressed in 0.5–1.0 mm buds and in 2.5–3.0 mm buds, respectively.  Among these, the expression levels of 14 miRNAs were higher and the levels of 23 miRNAs were lower in CN12A compared with CN12B.  The predicted target genes of these differentially expressed miRNAs encode protein kinases, F-box domain-containing proteins, MADS-box family proteins, SBP-box gene family members, HD-ZIP proteins, floral homeotic protein APETALA 2 (AP2), and nuclear factor Y, subunit A.  These targets have previously been reported to be involved in pollen development and male sterility, suggesting that miRNAs might act as regulators of GMS in rapeseed anthers.  Furthermore, RT-qPCR data suggest that one of the differentially expressed miRNAs, bna-miR159, plays a role in tapetal differentiation by regulating the expression of transcription factor BnMYB101 and participates in tapetal degradation and influences callose degradation by manipulating the expression of BnA6.  These findings contribute to our understanding of the roles of miRNAs during anther development and the occurrence of GMS in rapeseed.
 
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Expression and contribution of microphthalmia-associated transcription factor to the melanin deposition in Liancheng white ducks
XIN Qing-wu, MIAO Zhong-wei, LIU Zhao-yuan, LI Li, ZHANG Lin-li, ZHU Zhi-ming, ZHANG Zheng-hong, ZHENG Nen-zhu, WANG Zheng-chao
2020, 19 (3): 800-809.   DOI: 10.1016/S2095-3119(19)62736-X
Abstract101)      PDF in ScienceDirect      
The present study investigates the expression of microphthalmia-associated transcription factor (MITF) and its contribution to the melanin deposition in Liancheng white ducks.  Nested PCR was used to clone the MITF gene sequence from the skin tissue of female Liancheng white ducks.  Ultraviolet spectrophotometry was used to detect the melanin deposition.  MITF mRNA expression and melanin deposition in different tissues and organs were detected and their correlation was analyzed.  The MITF gene (GenBank number: MG516570) was 1 323 bp in length, contains a complete CDS region (34–1 323 bp) and codes 429 amino acids with 100% homology to the MITF of Anas platyrhynchos and over 95% homology to those of Gallus gallus and Coturnix japonica.  Genetic evolution analysis reveals a close relationship of Liancheng white ducks with A. platyrhynchos, and also to lesser extents with Anser cygnoides, silky fowl and G. gallus, as well as Sus scrofa, Ovis aries and other mammals.  Real-time quantitative PCR (qPCR) analysis demonstrated that MITF was expressed in skin, gizzard, liver, kidney and muscle, and of these tissues, its expression was the highest in the skin tissue (skin>gizzard>liver>kidney>muscle).  Ultraviolet spectrophotometry showed that melanin deposition was positively correlated with the MITF expression level in these five tissues and organs (P<0.05).  Together, these results demonstrated a tissue-specific pattern of MITF expression and a positive correlation between MITF expression and melanin deposition, indicating that MITF expression may contribute to the melanin deposition in Liancheng white ducks.
 
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Effect of tillage and burial depth and density of seed on viability and seedling emergence of weedy rice
ZHANG Zheng, GAO Ping-lei, DAI Wei-min, SONG Xiao-ling, HU Feng, QIANG Sheng
2019, 18 (8): 1914-1923.   DOI: 10.1016/S2095-3119(19)62583-9
Abstract183)      PDF in ScienceDirect      
Weedy rice (Oryza sativa f. spontanea) is one of the three worst paddy weeds in most rice growing areas.  The unexpected heavy infestation is derived from a persistence of soil seed bank of weedy rice, which the shattered seeds chiefly feed back to.  Information on soil seed bank dynamics is imperative to predict the infestation of weeds.  In the present paper, the effect of rotary tillage on weedy rice seed bank structure was studied first, and a burial experiment of marked seeds was conducted to observe the overwintering survival, seed viability and seedling emergence of weedy rice.  The results showed that the proportion of weedy rice seeds in deeper soil increased but seedling emergence decreased with increasing plowing depth.  The viability of weedy rice seeds decreased as the burial duration time extended but more slowly in deeper soil layers.  Additionally, there was no significant effect of burial density on seed viability.  Moreover, the logistic model fitted well (R2≥0.95, P≤0.01) with the depressive trends of seed viability with increasing burial time under all burial depths and densities which can provide us further information about seed survival.  In field experiments, number of seedling emergence significantly decreased as seed burial depth increased, conversely, proportion of seedling emergence increased as seed burial density decreased.  This study has important implications for determining strategies for weedy rice management by exhausting its seed bank through the alteration of tillage practices.
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Genetic diversity and population structure analysis of Capsicum germplasm accessions
GU Xiao-zhen, CAO Ya-cong, ZHANG Zheng-hai, ZHANG Bao-xi, ZHAO Hong, ZHANG Xiao-min, WANG Hai-ping, LI Xi-xiang, WANG Li-hao
2019, 18 (6): 1312-1320.   DOI: 10.1016/S2095-3119(18)62132-X
Abstract234)      PDF in ScienceDirect      
Genetic diversity plays an essential role in plant breeding and utilization.  Pepper is an important vegetable and spice crop worldwide.  The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables, Beijing, China was analyzed based on 29 simple sequence repeat (SSR) markers, which were evenly distributed over 12 pepper chromosomes.  The pepper accessions were divided into two groups in a genetic structure analysis, and the two groups showed obvious differences in fruit type and geographical distribution.  We finally selected 248 accessions capturing 75.6% of the SSR alleles as the core collection for further research.  Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.
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Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution
ZHANG Xiao-min, ZHANG Zheng-hai, GU Xiao-zhen, MAO Sheng-li, LI Xi-xiang, Jo?l Chadoeuf, Alain Palloix, WANG Li-hao, ZHANG Bao-xi
2016, 15 (9): 1991-2001.   DOI: 10.1016/S2095-3119(16)61364-3
Abstract1869)      PDF in ScienceDirect      
    Pepper (Capsicum spp.) is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world’s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 GenBank pepper accessions (local cultivars and landraces) from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat (SSR) markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages (UPGMA) in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.
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Cloning and characterization of CaGID1s and CaGAI in Capsicum annuum L.
CAO Ya-cong, ZHANG Zheng-hai, WANG Li-hao, SUI Xiao-lei, ZHANG Zhen-xian, ZHANG Bao-xi
2016, 15 (4): 775-784.   DOI: 10.1016/S2095-3119(15)61275-8
Abstract1374)      PDF in ScienceDirect      
Fruit set and development are affected by many phytohormones, including gibberellin.  Little is known regarding molecular mechanism underlying gibberellin mediated fruit set and development especially in Capsicum.  Three gibberellin receptors, CaGID1b.1, CaGID1b.2 and CaGID1c, and a DELLA protein, CaGAI, have been identified in Capsicum annuum L.  During the fruit development, the expression level of CaGID1c was low, and the expression fold change is mild.  However, CaGID1b.1 and CaGID1b.2 were relatively higher and more acute, which indicates that CaGID1b.1 and CaGID1b.2 may play an important role in fruit pericarp, placenta and seed.  Ectopic expressions of CaGID1b.1, CaGID1b.2 and CaGID1c in Arabidopsis double mutant gid1a gid1c increased plant height, among which CaGID1b.2 had the most significant effect; CaGAI reduced plant height in double mutant rga-24/gai-t6, having a similar function to AtGID1 and AtGAI in stem elongation.  Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that CaGID1b.1 and CaGID1b.2 interact with CaGAI in a GA-dependent manner, while CaGID1c interacts with CaGAI in a GA-independent manner.  Our study reveals the key elements during gibberellin signaling in Capsicum and supports the critical importance of gibberellin for Capsicum fruit set and development.
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Analysis of SSRs Information in Capsicum spp. from EST Database
HUANG Huan-huan, ZHANG Zhong-hua, ZHANG Zheng-hai, MAO Sheng-li, WANG Li-hao , ZHANG Bao-xi
2011, 10 (10): 1532-1536.   DOI: 10.1016/S1671-2927(11)60148-X
Abstract1988)      PDF in ScienceDirect      
SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pl’ software, while 116915 EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 microsatellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tri-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers.
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