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Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.)
LI Meng-wei, HE Yu-hua, LIU Rong, LI Guan, WANG Dong, JI Yi-shan, YAN Xin, HUANG Shu-xian, WANG Chen-yu, MA Yu, LIU Bei, YANG Tao, ZONG Xu-xiao
2023, 22 (9): 2648-2659.   DOI: 10.1016/j.jia.2023.01.003
Abstract237)      PDF in ScienceDirect      
Owing to the limitation of a large genome size (~13 Gb), the genetic and gene mapping studies on faba bean (Vicia faba L.) are lagging far behind those for other legumes.  In this study, we selected three purified faba bean lines (Yundou 8137, H0003712, and H000572) as parents and constructed two F2 populations.  These two F2 populations, namely 167 F2 plants in Pop1 (Yundou 8137×H0003712) and 204 F2 plants in Pop2 (H000572×Yundou 8137), were genotyped using a targeted next-generation sequencing (TNGS) genotyping platform, and two high-density single nucleotide polymorphisms (SNP) genetic linkage maps of faba bean were constructed.  The map constructed from Pop1 contained 5 103 SNPs with a length of 1 333.31 cM and an average marker density of 0.26 cM.  The map constructed from Pop2 contained 1 904 SNPs with a greater length of 1 610.61 cM.  In these two F2 populations, QTL mapping identified 98 QTLs for 14 agronomic traits related to the flowers, pods, plant types and grains.  The two maps were then merged into an integrated genetic linkage map containing 6 895 SNPs, with a length of 3 324.48 cM.  These results not only lay the foundation for fine mapping and map-based cloning of related genes, but can also accelerate the molecular marker-assisted breeding of faba bean.
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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
Abstract302)      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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Evaluation of the early defoliation trait and identification of resistance genes through a comprehensive transcriptome analysis in pears
SHAN Yan-fei, LI Meng-yan, WANG Run-ze, LI Xiao-gang, LIN Jing, LI Jia-ming, ZHAO Ke-jiao, WU Jun
2023, 22 (1): 120-138.   DOI: 10.1016/j.jia.2022.08.040
Abstract303)      PDF in ScienceDirect      

Early defoliation, which usually occurs during summer in pear trees, is gradually becoming a major problem that poses a serious threat to the pear industry in southern China.  However, there is no system for evaluating the responses of different cultivars to early defoliation, and our knowledge of the potential molecular regulation of the genes underlying this phenomenon is still limited.  In this study, we conducted field investigations of 155 pear accessions to assess their resistance or susceptibility to early defoliation.  A total of 126 accessions were found to be susceptible to early defoliation, and only 29 accessions were resistant.  Among them, 19 resistant accessions belong to the sand pear species (Pyrus pyrifolia).  To identify the resistance genes related to early defoliation, the healthy and diseased samples of two sand pear accessions, namely, the resistant early defoliation accession ‘Whasan’ and the susceptible early defoliation accession ‘Cuiguan’, were used to perform RNA sequencing.  Compared with ‘Cuiguan’, a total of 444 genes were uniquely differentially expressed in ‘Whasan’.  Combined with GO and KEGG enrichment analyses, we found that early defoliation was closely related to the stress response.  Furthermore, a weighted gene co-expression network analysis revealed a high correlation of WRKY and ethylene responsive factor (ERF) transcription factors with early defoliation resistance.  This study provides useful resistant germplasm resources and new insights into potentially essential genes that respond to early defoliation in pears, which may facilitate a better understanding of the resistance mechanism and molecular breeding of resistant pear cultivars

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Estimating daily actual evapotranspiration of a rice–wheat rotation system in typical farmland in the Huai River Basin using a two-step model and two one-step models
LI Meng, CHU Rong-hao, Abu Reza Md. Towfiqul ISLAM, JIANG Yue-lin, SHEN Shuang-he
2021, 20 (1): 274-288.   DOI: 10.1016/S2095-3119(20)63223-3
Abstract130)      PDF in ScienceDirect      
The objective of this study is to evaluate the performance of three models for estimating daily evapotranspiration (ET) by employing flux observation data from three years (2007, 2008 and 2009) during the growing seasons of winter wheat and rice crops cultivated in a farmland ecosystem (Shouxian County) located in the Huai River Basin (HRB), China.  The first model is a two-step model (PM−Kc); the other two are one-step models (e.g., Rana−Katerji (R−K) and advection-aridity (AA)).  The results showed that the energy closure degrees of eddy covariance (EC) data during winter wheat and rice-growing seasons were reasonable in the HRB, with values ranging from 0.84 to 0.91 and R2 of approximately 0.80.  Daily ET of winter wheat showed a slow decreasing trend followed by a rapid increase, while that of rice presented a decreasing trend after an increase.  After calibrating the crop coefficient (Kc), the PM–Kc model performed better than the model using the Kc recommended by the Food and Agricultural Organization (FAO).  The calibrated key parameters of the R−K model and AA model showed better universality.  After calibration, the simulation performance of the PM−Kc model was satisfactory.  Both the R−K model and AA model underestimated the daily ET of winter wheat and rice.  Compared with that of the R−K model, the simulation result of the AA model was better, especially in the simulation of daily ET of rice.  Overall, this research highlighted the consistency of the PM−Kc model to estimate the water demand for rice and wheat crops in the HRB and in similar climatic regions in the world. 
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Molecular and biological characterization of melon-infecting squash leaf curl China virus in China 
WU Hui-jie, LI Meng, HONG Ni, PENG Bin, GU Qin-sheng
2020, 19 (2): 570-577.   DOI: 10.1016/S2095-3119(19)62642-0
Abstract171)      PDF in ScienceDirect      
It has been reported that squash leaf curl China virus (SLCCNV) infects some Cucurbitaceae crops except for melon (Cucumis melo L.).  A new disease of melon exhibiting severe leaf curl and dwarfing was observed in Hainan Province of China.  In this study, the pathogen was identified as SLCCNV through biological and molecular characterization.  The isolate (SLCCNV-HN) possess a bipartite genome, DNA-A (HM566112.1) with the highest nucleotide identity (99%) to SLCCNV-Hn (MF062251.1) pumpkin and SLCCNV-Hn61 (AM260205.1) squash isolates from China, whereas DNA-B (HM566113.1) with the highest nucleotide identity (99%) to SLCCNV-Hn (MF062252.1).  Phylogenetic analyses based on the full-length SLCCNV-HN DNA-A and -B sequences indicated that SLCCNV-HN melon isolate is clustered with SLCCNV-Hn pumpkin, SLCCNV-Hn61 and SLCCNV-SY squash isolates from southern China, forming an independent cluster.  Infectious clone of SLCCNV-HN was constructed and the melon plants were inoculated and the infection rate is 100%, the systemic symptoms in melon showed identical to those of melon plants infected in fields.  Additionally, melon plants transmission of this virus by Bemisia tabaci with a transmission rate of 95% (19/20) showed leaf curl and dwarf symptoms 15 days post transmission, thereby fulfilling Koch’s postulates.  Analysis of genomic organization and phylogenetic trees indicated that SLCCNV-HN melon isolate belongs to the Begomovirus genus.  To the best of our knowledge, this is the first characterization of melon-infecting SLCCNV through its genome, infectious clone and transmission.
 
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Impact of cash crop cultivation on household income and migration decisions: Evidence from low-income regions in China
LI Meng, Christopher GAN, Wanglin MA, Wei JIANG
2020, 19 (10): 2571-2581.   DOI: 10.1016/S2095-3119(20)63161-6
Abstract156)      PDF in ScienceDirect      
This study examines the impact of cash crop cultivation on household income and migration decisions, using survey data collected from low-income regions in China.  Given farmers decide themselves whether to cultivate cash crops, an endogenous treatment regression model that accounts for potential selection bias issue is used to analyze the data.  The empirical results show that cash crop cultivation exerts a positive and statistically significant impact on household income, but it does not affect household migration decisions significantly.  The disaggregated analyses reveal that cash crop cultivation significantly increases farm income but decreases off-farm income.
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The effect of dehydrogenase enzyme activity in glycolysis on the colour stability of mutton during postmortem storage
XIN Jian-zeng, LI Zheng, LI Xin, LI Meng, WANG Ying, YANG Fu-min, ZHANG De-quan
2017, 16 (11): 2646-2654.   DOI: 10.1016/S2095-3119(16)61622-2
Abstract623)      PDF in ScienceDirect      
This study investigated the influence of activities of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and lactate dehydrogenase-B (LDH-B) on the colour stability of mutton.  From 60 sheep (Bayannur mutton sheep), 15 longissimus dorsi (LD) muscles were selected on the basis of colour stability (R630/580 and a* value) during the storage and classified into three groups (5 for each group) as high colour stability (HCS), intermediate colour stability (ICS) and low colour stability (LCS).  The activities of GAPDH and LDH-B, muscle colour attributes, nicotinamide adenine dinucleuotide (NADH) concentration and lactate concentration were measured.  The samples in HCS had higher activities of GAPDH and LDH-B than the samples in the LCS, and the samples in the HCS group also possessed higher NADH and lower lactate concentration.  The higher activity of dehydrogenase enzyme may result in higher NADH concentrations and colour stability in muscle tissue.  The results suggest that the activity of GAPDH and LDH-B may also play a role in maintaining colour stability.
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Effect of Zn application methods on Zn distribution and bioavailability in wheat pearling fractions of two wheat genotypes
LI Meng, TIAN Xiao-hong, LI Xiu-li, WANG Shao-xia
2017, 16 (07): 1617-1623.   DOI: 10.1016/S2095-3119(17)61657-5
Abstract787)      PDF in ScienceDirect      
Pearling is an effective method for evaluating the distribution of chemical components in wheat grain. Five pearling fractions (representing approximately 20% of the original sample weight) of wheat grain were obtained using the JNMJ3 rice polisher for two cultivars with different methods of Zinc (Zn) application; the residual portion (approximately 80%) was ground as flour. Results showed that foliar or soil+foliar Zn application methods effectively increased Zn concentrations and bioavailability in whole grain and pearling fractions, but soil Zn application was ineffective in field conditions. In addition, the concentrations of Zn, Fe, Mn and Cu within wheat grain showed a diminishing trend from the outer layer to the inner portions of the wheat grain as the pearling level increased. These results clearly showed the distribution of minerals in wheat grain, especially in the outer part of the grain (bran). The results also suggest that precise milling techniques combined with foliar Zn application could improve the Zn and Fe nutritional qualities of consumed flour and mitigate human Zn and Fe deficiencies.
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In vitro establishment of a highly effective method of castor bean (Ricinus communis L.) regeneration using shoot explants
ZHANG Ji-xing, WANG Xiao-yu, FENG Zi-zhou, GENG Xue-jun, MU Sha-moli, HUO Hong-yan, TONG Huan, LI Meng-zhu, LI Yi, CHI Yue, CHEN Yong-sheng
2016, 15 (06): 1417-1422.   DOI: 10.1016/S1671-2927(00)10558
Abstract1089)      PDF in ScienceDirect      
An efficient plant regeneration protocol was established for castor bean (Ricinus communis L.), in which 0.3 mg L–1 thidiazuron (TDZ) induced shoot clusters and increased the number of adventitious shoots from hypocotyl tissue. Our results showed that treatment under dark conditions significantly promoted the average number of shoots per explant to 37.36±4.54 (with a 6-d treatment). Modified 1/2 Murashige and Skoog (MS) basal medium supplemented with 440 mg L–1 Ca2+, 0.2 mg L–1 gibberellic acid and 0.1 mg L–1 TDZ significantly increased shoot elongation rates and lowered vitrification rates. Furthermore, 1/2 MS media supplemented with 0.2 mg L–1 1-naphthaleneacetic acid induced a higher rooting rate compared with other culture conditions.
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Studies on Methane Emissions from Pastoral Farming in New Zealand
LI Meng-meng, ZHANG Gui-guo, SUN Xue-zhao, DONG Shu-ting , Simone O Hoskin
2014, 13 (2): 365-377.   DOI: 10.1016/S2095-3119(13)60272-5
Abstract1722)      PDF in ScienceDirect      
The aim of this paper was to give a basic understanding of studies on methane emissions of New Zealand, as we know the agriculture of New Zealand is pastoral farming, most livestock animals are grazed in pasture, and quantities of methane were released from the digestive tract and animals excreta. In New Zealand some 50% greenhouse gases (GHG) sources are attributed to agriculture and one third is methane from livestock enteric formation. For many years, many researchers have been exploiting the techniques and methods to measure the emission of methane of New Zealand, further more studing the available options to alleviate the methane emissions. Their pioneering work and successful experiences including the determined methods and mitigation strategies are worth learning for scholars around the world. Some of their approaches were not only suitable for New Zealand grazed livestock, but for many other countries, even the animals are intensively bred in pen. The calorimeter/respiration chamber is the most exactly method in present, but it needs expensive equipments and skilled manipulators, so there are still some difficulty in applying this approach extensively in practice. Sulfur hexafluoride (SF6) trace technique is much adopted for grazed livestock evaluating the methane emission, though its veracity was doubted by some researchers, it is still a good option in present for studying the GHG emissions for grazing animals. By measuring the rumen volatile fatty acid (VFA) concentration to estimate the methane emission is a relatively simple approach, it is just only a rough evaluation, and it is unsuitable for exact study, but this method may be used in China for extensively raised ruminant. In present China, the ruminants are fed in an extensively managed state, the diversities of roughage and animals varieties caused difficult to exactly estimate the methane emission. So exploiting the available options is much important for constituting the exhaustive emission inventory. This review just outline some practical techniques of New Zealand, those maybe a good reference for researchers to carry out their studies in this field, after all New Zealand have been persisting many years and acquired great achievements in methane mitigation area.
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Mapping of QTL Associated with Drought Tolerance in a Semi-Automobile Rain Shelter in Maize (Zea mays L.)
ZHU Jing-jing*, WANG Xiao-peng*, SUN Cui-xia, ZHU Xiu-miao, LI Meng, ZHANG Guo-dong, TIAN Yanchen, WANG Ze-li
2011, 10 (7): 987-996.   DOI: 10.1016/S1671-2927(11)60085-0
Abstract2050)      PDF in ScienceDirect      
Drought is a major constraint in maize production worldwide. We studied quantitative trait loci (QTL) underlying droughttolerance for maize plants grown in two different environments. Traits investigated included ASI, plant height, grain yield,ear height, and ear setting. A genetic linkage map was constructed with 120 simple sequence repeat (SSR) markers basedon an F2 population derived from a cross between D5 (resistant parent) and 7924 (susceptible parent). Correlation andheritability were calculated. QTLs of these traits were identified by composite interval mapping combined with a linkagemap covering 1 790.3 cM. The markers were arranged in ten linkage groups. QTL mapping was made of the mean traitperformance of the 180 F2:3 population. The results showed five, five, six, four, and five QTLs for ASI, plant height, grainyield, ear height, and ear setting under full irrigation condition, respectively, and four, seven, six, four, and four QTLs forASI, plant height, grain yield, ear height, and ear setting under severe late stress conditions, respectively. Especially thefour QTLs detected for five traits in 2008 and 2009. The universal QTLs information generated in this study will aid inundertaking an integrated breeding strategy for further genetic studies in drought tolerance improvement in maize.
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