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1. Synonymous codon usage pattern in model legume Medicago truncatula
SONG Hui, LIU Jing, CHEN Tao, NAN Zhi-biao
Journal of Integrative Agriculture    2018, 17 (09): 2074-2081.   DOI: 10.1016/S2095-3119(18)61961-6
摘要360)      PDF    收藏
Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution.  Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula.  In present study, 39 531 available coding sequences (CDSs) from M. truncatula were examined for codon usage bias (CUB).  Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB.  We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage.  These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively.  Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs.  The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content.  Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.
 
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2. How plant density affects maize spike differentiation, kernel set, and grain yield formation in Northeast China?
ZHANG Ming, CHEN Tao, Hojatollah Latifmanesh, FENG Xiao-min, CAO Tie-hua, QIAN Chun-rong, DENG Ai-xing, SONG Zhen-wei, ZHANG Wei-jian
Journal of Integrative Agriculture    2018, 17 (08): 1745-1757.   DOI: 10.1016/S2095-3119(17)61877-X
摘要508)      PDF    收藏
Received  14 August, 2017    Accepted  20 December, 2017
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3. Research progress on the breeding of japonica super rice varieties in Jiangsu Province, China
WANG Cai-lin, ZHANG Ya-dong, ZHU Zhen, CHEN Tao, ZHAO Qing-yong, ZHONG Wei-gong, YANG Jie, YAO Shu, ZHOU Li-hui, ZHAO Ling, LI Yu-sheng
Journal of Integrative Agriculture    2017, 16 (05): 992-999.   DOI: 10.1016/S2095-3119(16)61580-0
摘要1173)      PDF    收藏
In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences.  We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency.  The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program.  It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.
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4. Optimization of Two-Dimensional Gel Electrophoresis for Kenaf Leaf Proteins
CHEN Tao, QI Jian-min, XU Jian-tang, CHEN Pin-pin, TAO Ai-fen, CHEN Fu-cheng , CHEN Wei
Journal of Integrative Agriculture    2011, 10 (12): 1842-1850.   DOI: 10.1016/S1671-2927(11)60184-3
摘要1711)      PDF    收藏
To establish a suitable and effective protocol of protein extraction for two-dimensional gel electrophoresis (2-DE) analysis in kenaf leaf tissues, three extraction methods (trichloroacetic acid/acetone, urea/thiourea, and phenol extraction methods) were applied to the extraction of kenaf leaf protein. The results were compared in regard to protein extraction efficiency, sodiumdodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and 2-DE gels. Furthermore, the 2-DE system was optimized for four aspects: the pH range of IPG (immobilized pH gradient) stripes, sampling methods, sample volumes, and concentration of polyacrylamide gels. The data presented showed that the phenol extraction method is the best method to perform 2-DE analysis of kenaf leaf protein. The protein extracted from phenol extraction method reached the purity of (26.40±0.859)%, showed (25.67±1.53) protein bands in one dimension SDS-PAGE gels, and (1 374±54.44) protein spots on 2-DE gels. The research also indicates that kenaf leaf protein spots were distributed mainly within the pH range of 4-8. More clear background with a better distribution effect and many protein spots could be obtained on 2-DE gels under the conditions of active rehydration loading, 24 cm IPG strips (linear pH gradient of 4-7), 1.4 mg samples, and 12% SDS-PAGE gels.
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