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A comprehensive evaluation of factors affecting the accuracy of pig genotype imputation using a single or multi-breed reference population
ZHANG Kai-li, PENG Xia, ZHANG Sai-xian, ZHAN Hui-wen, LU Jia-hui, XIE Sheng-song, ZHAO Shu-hong, LI Xin-yun, MA Yun-long
2022, 21 (2): 486-495.   DOI: 10.1016/S2095-3119(21)63695-X
Abstract281)      PDF in ScienceDirect      
Genotype imputation has become an indispensable part of genomic data analysis.  In recent years, imputation based on a multi-breed reference population has received more attention, but the relevant studies are scarce in pigs.  In this study, we used the Illumina PorcineSNP50 Bead Chip to investigate the variations of imputation accuracy with various influencing factors and compared the imputation performance of four commonly used imputation software programs.  The results indicated that imputation accuracy increased as either the validation population marker density, reference population sample size, or minor allele frequency (MAF) increased.  However, the imputation accuracy would have a certain extent of decrease when the pig reference population was a mixed group of multiple breeds or lines.  Considering both imputation accuracy and running time, Beagle 4.1 and FImpute are excellent choices among the four software packages tested.  This work visually presents the impacts of these influencing factors on imputation and provides a reference for formulating reasonable imputation strategies in actual pig breeding.
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Quantifying key model parameters for wheat leaf gas exchange under different environmental conditions
ZHAO Fu-nian, ZHOU Shuang-xi, WANG Run-yuan, ZHANG Kai, WANG He-ling, YU Qiang
2020, 19 (9): 2188-2205.   DOI: 10.1016/S2095-3119(19)62796-6
Abstract126)      PDF in ScienceDirect      
The maximum carboxylation rate of Rubisco (Vcmax) and maximum rate of electron transport (Jmax) for the biochemical photosynthetic model, and the slope (m) of the Ball-Berry stomatal conductance model influence gas exchange estimates between plants and the atmosphere.  However, there is limited data on the variation of these three parameters for annual crops under different environmental conditions.  Gas exchange measurements of light and CO2 response curves on leaves of winter wheat and spring wheat were conducted during the wheat growing season under different environmental conditions.  There were no significant differences for Vcmax, Jmax or m between the two wheat types.  The seasonal variation of Vcmax, Jmax and m for spring wheat was not pronounced, except a rapid decrease for Vcmax and Jmax at the end of growing season.  Vcmax and Jmax show no significant changes during soil drying until light saturated stomatal conductance (gssat) was smaller than 0.15 mol m–2 s–1.  Meanwhile, there was a significant difference in m during two different water supply conditions separated  by gssat at 0.15 mol m–2 s–1.  Furthermore, the misestimation of Vcmax and Jmax had great impacts on the net photosynthesis rate simulation, whereas, the underestimation of m resulted in underestimated stomatal conductance and transpiration rate and an overestimation of water use efficiency.  Our work demonstrates that the impact of severe environmental conditions and specific growing stages on the variation of key model parameters should be taken into account for simulating gas exchange between plants and the atmosphere.  Meanwhile, modification of m and Vcmax (and Jmax) successively based on water stress severity might be adopted to simulate gas exchange between plants and the atmosphere under drought.
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Bioinformatic analysis and functional characterization of the cfem proteins in maize anthracnose fungus Colletotrichum graminicola
GONG An-dong, JING Zhong-ying, ZHANG Kai, TAN Qing-qun, WANG Guo-liang, LIU Wen-de
2020, 19 (2): 541-550.   DOI: 10.1016/S2095-3119(19)62675-4
Abstract161)      PDF in ScienceDirect      
Fungal secreted proteins that contain the Common in Fungal Extracellular Membrane (CFEM) domain are important for pathogenicity.  The hemibiotrophic fungus Colletotrichum graminicola causes the serious anthracnose disease of maize.  In this study, we identified 24 CgCFEM proteins in the genome of C. graminicola.  Phylogenic analysis revealed that these 24 proteins (CgCFEM1–24) can be divided into 2 clades based on the presence of the trans-membrane domain.  Sequence alignment analysis indicated that the amino acids of the CFEM domain are highly conserved and contain 8 spaced cysteines, with the exception that CgCFEM1 and CgCFEM24 lack 1 and 2 cysteines, respectively.  Ten CgCFEM proteins with a signal peptide and without the trans-membrane domain were considered as candidate effectors and, thus were selected for structural prediction and functional analyses.  The CFEM domain in the candidate effectors can form a helical-basket structure homologous to the Csa2 protein in Candida albicans, which is responsible for haem acquisition and pathogenicity.  Subcellular localization analysis revealed that these effectors accumulate in the cell membrane, nucleus, and cytosolic bodies.  Additionally, 5 effectors, CgCFEM6, 7, 8, 9 and 15, can suppress the BAX-induced programmed cell death in Nicotiana benthamiana with or without the signal peptide.  These results demonstrate that these 10 CgCFEM candidate effectors with different structures and subcellular localizations in host cells may play important roles during the pathogenic processes on maize plants.
 
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Effects of Paranosema locustae (Microsporidia) on the development and morphological phase transformation of Locusta migratoria (Orthoptera: Acrididae) through modulation of the neurotransmitter taurine
LI Ao-mei, YIN Yue, ZHANG Yu-xin, ZHANG Liu, ZHANG Kai-qi, SHEN Jie, TAN Shu-qian, SHI Wang-peng
2020, 19 (1): 204-210.   DOI: 10.1016/S2095-3119(19)62637-7
Abstract106)      PDF in ScienceDirect      
Neurotransmitters are important in the maintenance of phase transformation of Locusta migratoria (Arthropoda: Orthoptera).  Here, the effects of the entomopathogen Paranosema locustae on the neurotransmitter taurine in migratory locusts were studied using biochemical methods.  After inoculation with P. locustae, the taurine content of infected locusts significantly declined, but F/C values (ratio between the length of hind femur and the width of the head of locust) increased significantly, compared to healthy locusts.  Meanwhile, F/C values of infected locusts that were injected with 2 µg of taurine showed no significant differences from those of healthy locusts, demonstrating that supplemental taurine inhibited the changes in morphological phase caused by P. locustaeParanosema locustae infection also caused longer developmental durations and lower body weights of locusts, but these changes were unaffected after injection with taurine.  These results provided new insights into the mechanisms by which microsporidian parasites affected their locust hosts.
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Effects of different LEDs light spectrum on the growth, leaf anatomy, and chloroplast ultrastructure of potato plantlets in vitro and minituber production after transplanting in the greenhouse
CHEN Li-li, ZHANG Kai, GONG Xiao-chen, WANG Hao-ying, GAO You-hui, WANG Xi-quan, ZENG Zhao-hai, HU Yue-gao
2020, 19 (1): 108-119.   DOI: 10.1016/S2095-3119(19)62633-X
Abstract162)      PDF in ScienceDirect      
Light spectrum plays an important role in regulating the growth and development of in vitro cultured potato (Solanum tuberosum L.) plantlets.  The status of potato plantlets at the end of in vitro stage influences the minituber production after transplanting.  With 100 μmol m–2 s–1 total photosynthetic photon flux density (PPFD), a light spectrum study of 100% red light emitting diodes (LEDs) light spectrum (RR), 100% blue LEDs light spectrum (BB), 65% red+35% blue LEDs light spectrum (RB), and 45% red+35% blue+20% green LEDs light spectrum (RBG) providing illumination at the in vitro cultured stage of potato plantlets for 4 weeks using fluorescent lamp as control (CK) was performed to investigate the effects of LEDs light spectrum on the growth, leaf anatomy, and chloroplast ultrastructure of potato plantlets in vitro as well as the minituber yield after 2 months transplanting in the greenhouse.  Compared to CK, RB and RBG promoted the growth of potato plantlets in vitro with increased stem diameter, plantlet fresh weight, plantlet dry weight, and health index.  Furthermore, BB induced the greatest stem diameter as well as the highest health index in potato plantlets in vitro.  Root activity, soluble protein, and free amino acid were also significantly enhanced by BB, whereas carbohydrates were improved by RR.  In addition, thickness of leaf, palisade parenchyma and spongy parenchyma was significantly increased by BB and RBG.  Chloroplasts under BB and RBG showed well-developed grana thylakoid and stroma thylakoid.  Unexpectedly, distinct upper epidermis with greatest thickness was induced and palisade parenchyma and spongy parenchyma were arranged neatly in RR.  After transplanting in the greenhouse for 2 months, potato plantlets in vitro from BB, RB, and RBG produced high percentage of large size tuber.  BB improved fresh and dry weights of the biggest tuber but decreased tuber number per plantlet.  In addition, RBG increased tuber number as well as tuber fresh and dry weight slightly.  Our results suggested monochromatic blue LEDs as well as combined red, blue or/and green LEDs light spectrum were superior to fluorescent lamp spectrum in micro-propagation of potato plantlets.  Therefore, the application of RBG was suitable; BB and RB could be used as alternatives.
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Estimates on nitrogen uptake in the subsequent wheat by above-ground and root residue and rhizodeposition of using peanut labeled with 15N isotope on the North China Plain
ZHANG Kai, ZHAO Jie, WANG Xi-quan, XU He-shui, ZANG Hua-dong, LIU Jing-na, HU Yue-gao, ZENG Zhao-hai
2019, 18 (3): 571-579.   DOI: 10.1016/S2095-3119(18)62112-4
Abstract262)      PDF (449KB)(205)      
Leguminous crops play a vital role in enhancing crop yield and improving soil fertility.  Therefore, it can be used as an organic N source for improving soil fertility.  The purpose of this study was to (i) quantify the amounts of N derived from rhizodeposition, root and above-ground biomass of peanut residue in comparison with wheat and (ii) estimate the effect of the residual N on the wheat-growing season in the subsequent year.  The plants of peanut and wheat were stem fed with 15N urea using the cotton-wick method at the Wuqiao Station of China Agricultural University in 2014.  The experiment consisted of four residue-returning strategies in a randomized complete-block design: (i) no return of crop residue (CR0); (ii) return of above-ground biomass of peanut crop (CR1); (iii) return of peanut root biomass (CR2); and (iv) return of all residue of the whole peanut plant (CR3).  The 31.5 and 21% of the labeled 15N isotope were accumulated in the above-ground tissues (leaves and stems) of peanuts and wheat, respectively.  N rhizodeposition of peanuts and wheat accounted for 14.91 and 3.61% of the BG15N, respectively.  The 15N from the below-ground 15N -labeled of peanuts were supplied 11.3, 5.9, 13.5, and 6.1% of in the CR0, CR1, CR2, and CR3 treatments, respectively.  Peanut straw contributes a significant proportion of N to the soil through the decomposition of plant residues and N rhizodeposition.  With the current production level on the NCP, it is estimated that peanut straw can potentially replace 104 500 tons of synthetic N fertilizer per year.  The inclusion of peanut in rotation with cereal can significantly reduce the use of N fertilizer and enhance the system sustainability.

 
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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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Molecular characterization and tissue expression profile of the Dnmts gene family in pig
LUO Zong-gang, ZHANG Kai, CHEN Lei, YANG Yuan-xin, FU Peng-hui, WANG Ke-tian, WANG Ling, LI Ming-zhou, LI Xue-wei, ZUO Fu-yuan, WANG Jin-yong
2017, 16 (06): 1367-1374.   DOI: 10.1016/S2095-3119(16)61512-5
Abstract803)      PDF in ScienceDirect      
DNA methyltransferases (Dnmts) comprise a family of proteins which involved in the establishment and maintenance of DNA methylation patterns.  In pig, the molecular characterization and tissue expression profile of Dnmt gene family are not clear.  To solve this problem, reverse transcriptase PCR and rapid amplification of cDNA ends were used to clone the sequences of the porcine Dnmt2 and Dnmt3b genes.  Furthermore, the mRNA expression profiles of Dnmt1, Dnmt2, Dnmt3a and Dnmt3b genes from 54 adult tissues and 2 entire fetuses of Rongchang pig were analyzed by quantitative real-time PCR (qRT-PCR).  As a result, the lengths of porcine Dnmt2 and Dnmt3b gene cDNAs were 1 227 and 2 559 bp with cytosine-C5 specific DNA methylase domain, respectively.  The four Dnmt genes were highly expressed in longissimus dorsi muscle (P<0.01).  Dnmt1 is highly expressed in heart (P<0.01) and Dnmt 2 shows its preference in liver and seminal vesicle tissue (P<0.01).  Dnmt3a and Dnmt3b are highly expressed in the two fetus stages (P<0.01).  All these results suggested that each gene has its specific expression profile, and deeper study is required to dig more details between the methylation level and Dnmt family mRNA expressions in different tissues.
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Winter cover crops alter methanotrophs community structure in a double-rice paddy soil
LIU Jing-na, ZHU Bo, YI Li-xia, DAI Hong-cui, XU He-shui, ZHANG Kai, HU Yue-gao, ZENG Zhao-hai
2016, 15 (3): 553-565.   DOI: 10.1016/S2095-3119(15)61206-0
Abstract2200)      PDF in ScienceDirect      
Methanotrophs play a vital role in the mitigation of methane emission from soils. However, the influences of cover crops incorporation on paddy soil methanotrophic community structure have not been fully understood. In this study, the impacts of two winter cover crops (Chinese milk vetch (Astragalus sinicus L.) and ryegrass (Lolium multiflorum Lam.), representing leguminous and non-leguminous cover crops, respectively) on community structure and abundance of methanotrophs were evaluated by using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and real-time PCR technology in a double-rice cropping system from South China. Four treatments were established in a completely randomized block design: 1) double-rice cropping without nitrogen fertilizer application, CK; 2) double-rice cropping with chemical nitrogen fertilizer application (200 kg ha–1 urea for entire double-rice season), CF; 3) Chinese milk vetch cropping followed by double-rice cultivation with Chinese milk vetch incorporation, MV; 4) ryegrass cropping followed by double-rice cultivation with ryegrass incorporation, RG. Results showed that cultivating Chinese milk vetch and ryegrass in fallow season decreased soil bulk density and increased rice yield in different extents by comparison with CK. Additionally, methanotrophic bacterial abundance and community structure changed significantly with rice growth. Methanotrophic bacterial pmoA gene copies in four treatments were higher during late-rice season (3.18×107 to 10.28×107 copies g–1 dry soil) by comparison with early-rice season (2.1×107 to 9.62×107 copies g–1 dry soil). Type I methanotrophs absolutely predominated during early-rice season. However, the advantage of type I methanotrophs kept narrowing during entire double-rice season and both types I and II methanotrophs dominated at later stage of late-rice.
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ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato (Ipomoea batatas L.) in China
ZHANG Kai, WU Zheng-dan, LI Yan-hua, ZHANG Han, WANG Liang-ping, ZHOU Quan-lu, TANG Dao-bin, FU Yu-fan, HE Feng-fa, JIANG Yu-chun, YANG Hang , WANG Ji-chun
2014, 13 (11): 2346-2361.   DOI: 10.1016/S2095-3119(14)60779-6
Abstract1242)      PDF in ScienceDirect      
To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat (ISSR) markers. The mean genetic similarity coefficient, Nei’s gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and five subpopulations based on neighbor-joining (NJ) clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identified. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to flesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance (AMOVA) revealed small but significant difference between white and orange-fleshed sweet potato accessions. Small but significant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.
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