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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. GGE biplot analysis of yield stability and test location representativeness in proso millet (Panicum miliaceum L.) genotypes
ZHANG Pan-pan, SONG Hui, KE Xi-wang, JIN Xi-jun, YIN Li-hua, LIU Yang, QU Yang, SU Wang, FENG Nai-jie, ZHENG Dian-feng, FENG Bai-li
Journal of Integrative Agriculture    2016, 15 (06): 1218-1227.   DOI: 10.1016/S2095-3119(15)61157-1
摘要1637)      PDF    收藏
    The experiments were conducted for three consecutive years across 14 locations using 9 non-waxy proso millet genotypes and 16 locations using 7 waxy proso millet genotypes in China. The objectives of this study were to analyze yield stability and adaptability of proso millets and to evaluate the discrimination and representativeness of locations by analysis of variance (ANOVA) and genotype and genotype by environment interaction (GGE) biplot methods. Grain yields of proso millet genotypes were significantly influenced by environment (E), genotype (G) and their interaction (G×E) (P<0.1%). G×E interaction effect was six times higher than G effect in non-waxy group and seven times in waxy group. N04-339 in non-waxy and Neimi 6 (NM6) in waxy showed higher grain yields and stability compared with other genotypes. Also, Neimi 9 (NM9, a non-waxy cultivar) and 90322-2-33 (a waxy cultivar) showed higher adaptability in 7 and in 11 locations, respectively. For non-waxy, Dalat, Inner Mongolia (E2) and Wuzhai, Shanxi (E5) were the best sites among all the locations for maximizing the variance among candidate cultivars, and Yanchi, Ningxia (E10) had the best representativeness. Wuzhai, Shanxi (e9) and Yanchi, Ningxia (e14) were the best representative locations, and Baicheng, Jilin (e2) was better discriminating location than others for waxy genotypes. Based on our results, E10 and e14 have enhanced efficiency and accuracy for non-waxy genotypes and waxy genotypes selection, respectively in national regional test of proso millet varieties.
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3. Relations Between Photosynthetic Parameters and Seed Yields of Adzuki Bean Cultivars (Vigna angularis)
SONG Hui, GAO Jin-feng, GAO Xiao-li, DAI Hui-ping, ZHANG Pan-an, FENG Bai-li, WANG Peng-ke
Journal of Integrative Agriculture    2012, 12 (9): 1453-1461.   DOI: 10.1016/S1671-2927(00)8677
摘要1472)      PDF    收藏
The study comparatively examined the leaf photosynthetic capacities of different adzuki bean cultivars, high-yield 2000-75 and Jihong 9218, and low-yield Hongbao 1 and Wanxuan 1 from flowering to ripening. It showed that after flowering, the leaves of the cultivars gradually aged, the leaf chlorophyll (Chl.), soluble protein (SP) contents, net photosynthetic rates (Pn), transpiration rates (Tr) and stomatal conductance (Gs) of the cultivars tended to decline, but the leaf intercellular CO2 concentration (Ci) of the cultivars tended to rise. The leaf photosynthetic capacities of the cultivars decreased gradually from the lower to the upper nodes. The dry seed yields of the cultivars were positively correlated with their leaf Chl., SP, Pn, and Tr and Gs, and negatively associated with their leaf Ci. At the late growth stages, the high-yield cultivars maintained higher leaf Chl. contents, SP contents, Pn, Tr, and Gs than the low-yield cultivars, indicating that leaf photosynthetic capacity was one of important yield-affecting factors of adzuki bean. Therefore, it was important for a crop at the crucial stage of yield formation to maintain a high leaf chlorophyll content and a high leaf photosynthetic capacity and delay leaf aging.
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