水稻分蘖逆制的可塑性生长发育试验和模型辅助分析: 应用植物生长模型缩减基因型与表现型的间隙

表现型是基因型和环境相互作用的结果，不同环境条件下给定基因型能表达为不同的表型，这是我们所熟知的植物表型可塑性。可塑性一方面帮助植物更好地适应不利环境，但我们也不得不承认可塑性，使得人们难以从表型直接理解基因功能。如今，基因组学快速发展允许解密基因更迅速便捷，甚至发现大量基因。因此，进一步理解可塑性过程的基因背景、理解基因和环境对表型的作用非常必要。由于从基因到表型非线性过程，从而引起基因型和表型差异，期望有效方法或工具能跨越这个横沟。植物生长模型已被开发用来模拟植物响应环境动态关系，并且将参数和环境整合到模型方法中。因此，普遍认为植物生长模型将在探讨复杂可塑性基因功能扮演重要作用。水稻是普遍应用在基因组学和功能基因组学典型的模式植物。水稻分蘖是重要的基因依赖环境敏感的过程，这是农学上非常关注的现象。本文将应用模型方法理解水稻分蘖逆制的可塑性。本研究设计了一个相对优化环境条件下，野生型水稻分蘖逆制试验，该试验有两个处理（1）手工剪切分蘖;（2）一个TDNA突变体，并分别设置对照。本试验在法国国际农业研究发展中心（CIRAD）温室开展，每个试验利用水培方法，培育植株50天左右（营养生长阶段）。在营养生长阶段，定期破坏性测量单个器官的鲜重、干重和单个器官的大小。本文尝试应用两个植物生长模型模拟和解释水稻响应分蘖逆制表型发育。GreenLab是一个植物结构数学模型，已被开发用来模拟植物结构动态和结构功能反馈。植物3D结构决定光捕获和生物产量，然后，生物量分配到新的器官，因此，器官形态结构将发生变化，新阶段的生物量生产将会更新。通过基于最小二乘法的CornerFit软件实现了模型参数优化。另一个模型EcoMeristem，基于作物模型和形态发生概念，用来模拟水稻分生组织活动、器官发生和形态过程等可塑性过程，内部竞争指数Ic主要与环境相关，参数主要描述基因功能。通过植物生长过程模拟与测量的优化，手工提取了模型参数。这两个植物生长模型演示了缩减基因型与表型之间的差距，并实现了水稻响应分蘖完全逆制的可塑性过程。GreenLab模型有一个极好的器官发生基础，但本研究限于单茎拓扑结构。另外，该模型有更长的时间步长，这对描述植物可塑性没有提供足够的分辨能力，这在EcoMeristem模型中得到了解决。很明显，EcoMeristem模型有更弱的结构基础，这可能蕴含了一些可塑性信息的缺失。总体而言，EcoMeristem模型有更专业的可塑性过程、基因环境理解和表达能力。

The role of MC1R gene in buffalo coat color

Melanocortin-1 receptor (MC1R) plays a major role in pigmentation in many species. To investigate if the MC1R gene is associated with coat color in water buffalo, the coding region of MC1R gene of 216 buffalo samples was sequenced, which included 49 black river buffalo (Murrah and Nili-Ravi), 136 swamp buffalo (Dehong, Diandongnan, Dechang, Guizhou, and Xilin) with white and gray body, and 31 hybrid offspring of river buffalo Nili-Ravi (or Murrah) and swamp buffalo. Among the three variation sites found, SNP684 was synonymous, while SNP310 and SNP384 were nonsynonymous, leading to p.S104G and p.I128M changes, respectively. Only Individuals carrying homozygote E-BR/E-BR were black. The genotype and phenotype analysis of the hybrid offspring of black river buffalo and gray swamp buffalo further revealed that the river buffalo type allele E-BR or the allele carrying the amino acid p.104S was important for the full function of MC1R. The in silico functional analysis showed that the amino acid substitutions p.G104S and p.M128I had significant impact on the function of MC1R. Above results indicate that the allele E-BR or the allele carrying the amino acid p.104S was associated with the black coat color in buffalo.

The polymorphism of lysozyme gene in Zhikong scallop (Chlamys farreri) and its association with susceptibility/resistance to Listonella anguillarum

Lysozyme functions as a crucial biodefence effector against the infection of bacterial pathogens in innate immunity. The nucleotide sequence polymorphisms in promoter region of a nuclear goose type lysozyme gene from Zhikong scallop Chlamys farreri (designated as CFLysG) were investigated to explore their association with susceptibility/resistance to Listonella anguillarum infection. Eight sites of single nucleotide polymorphisms (SNPs) and two sites of insert-deletion (ins-del) polymorphisms were identified in the promoter region of CFLysG. Two of them, -753 TATCTCGATCAGG ins-del polymorphism and -391 A-G SNP were selected to analyze their distribution in the susceptible and resistant stocks, which were identified according to the survival time after L. anguillarum challenge. Using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), two genotypes were found at each site, which were ins/del and ins/ins at locus -753, and A/A and A/G at locus -391, respectively. The -753 ins/del genotype was more prevalent in the resistant stock than that in the susceptible stock, 30% vs 16.67% in frequency, but there was no significant difference in the frequency distribution between these two stocks (P=0.15). In contrast, the frequency of -391A/G genotype in the resistant stock was significantly higher (30%) than that in the susceptible stock (7.14%) (P=0.007), indicating a significant association with the resistance of Zhikong scallop to L anguillarum. To confirm the presumption, another independent challenge experiment was performed, in which the cumulative mortality of scallops with -391 A/A genotype (96.8%) was significantly higher than those with -391 A/G genotype (64.5%) (P=0.001), which further validate the association between -391 A/G genotype and the resistance of Zhikong scallop to L anguillarum. These results suggested that the -391 A/G could be a potential marker applied in future selection of Zhikong scallop with enhanced resistance to L anguillarum. (C) 2008 Elsevier Ltd. All rights reserved.

Molecular basis of transferrin polymorphism in goldfish (Carassius auratus)

Transferrin (TF) polymorphism was investigated in a color variety of goldfish (Carassius auratus), and its molecular basis analyzed. Three TF variants (A(1), A(2) and B-1) were identified from an inbred strain of the goldfish, of which A(1) and B-1 displayed a large electrophoretic difference on both native and SDS-PAGE gels. The TF cDNAs corresponding to variants A(1) and B-1 were cloned and sequenced from A(1)A(1), A(1)B(1) and B1B1 individuals, and their deduced amino acid sequences were analyzed. Substantial amino acid variation occurred between variants A(1) and B-1, with significant differences in peptide length, theoretical molecular weight (Mw) and isoelectric point (pI). No potential glycosylation sites were observed in the two amino acid sequences, which excluded the possibility that carbohydrate difference might cause electrophoretic variation among the TF variants. Further analysis suggested that the distinct electrophoretic mobility of the two variants A(1) and B-1 by SDS-PAGE resulted from their Mw difference, while the difference by the native PAGE could be explained by their pI variation. Furthermore, genomic DNA fragments containing the transferrin alleles were amplified and subjected to RFLP analysis in A(1)A(1), A(1)B(1) and B1B1 individuals. The data revealed characteristic banding patterns for each TF genotype, and demonstrated that the TF alleles A(1) and B-1 could be used as a co-dominant marker system. The initial work relating to the goldfish TF variants will benefit the understanding of the evolutionary and functional significance of TF polymorphism in fish.

两种施氮水平下不同基因型冬小麦叶片光合特性与形态差异的研究

田间试验研究不施N和施N(90kg/hm2)条件下“NR9405”、“9430”、“偃师9号”、“小偃6号”、“陕229”、“西农2208”、“矮丰3号”和“商188”等8种不同基因型冬小麦中后期生理特性及其叶片形态的差异结果表明,抽穗期倒二叶和灌浆期旗叶的净光合速率、气孔导度、蒸腾速率及瞬时水分利用效率在不同基因型间存在显著差异,施N仅能显著降低抽穗期倒二叶的蒸腾速率,而对功能叶的其他生理指标无明显影响。小麦成熟期旗叶和倒二叶的长度、宽度及叶面积在不同基因型间也存在极显著差异,施N对这些叶片形态指标有极显著地促进作用,基因型和N肥同时影响灌浆期旗叶的SPAD值,而叶片衰老指数主要受基因型调控。总体上看,冬小麦叶片形态指标同时受施N和基因型影响,而生理指标主要受基因型影响,N肥的影响相对较小。

Diffusive coevolution and mutualism maintenance mechanisms in a fig-fig wasp system

In reciprocal mutualism systems, the exploitation events by exploiters might disrupt the reciprocal mutualism, wherein one exploiter species might even exclude other coexisting exploiter species over an evolutionary time frame. What remains unclear is how such a community is maintained. Niche partitioning, or spatial heterogeneity among the mutualists and exploiters, is generally believed to enable stability within a mutualistic system. However, our examination of a reciprocal mutualism between a fig species (Ficus racemosa) and its pollinator wasp (Ceratosolen fusciceps) shows that spatial niche partitioning does not sufficiently prevent exploiters from overexploiting the common resource (i.e., the female flowers), because of the considerable niche overlap between the mutualists and exploiters. In response to an exploiter, our experiment shows that the fig can (1) abort syconia-containing flowers that have been galled by the exploiter, Apocryptophagus testacea, which oviposits before the pollinators do; and (2) retain syconia-containing flowers galled by Apocryptophagus mayri, which oviposit later than pollinators. However, as a result of (2), there is decreased development of adult non-pollinators or pollinator species in syconia that have not been sufficiently pollinated, but not aborted. Such discriminative abortion of figs or reduction in offspring development of exploiters while rewarding cooperative individuals with higher offspring development by the fig will increase the fitness of cooperative pollinating wasps, but decrease the fitness of exploiters. The fig fig wasp interactions are diffusively coevolved, a case in which fig wasps diversify their genotype, phenotype, or behavior as a result of competition between wasps, while figs diverge their strategies to facilitate the evolution of cooperative fig waps or lessen the detrimental behavior by associated fig wasps. In habitats or syconia that suffer overexploitation, discriminative abortion of figs or reduction in the offspring development of exploiters in syconia that are not or not sufficiently pollinated will decrease exploiter fitness and perhaps even drive the population of exploiters to local extinction, enabling the evolution and maintenance of cooperative pollinators through the movement between habitats or syconia (i.e., the metapopulations).

Phenotype and Function of Monocyte-Derived Dendritic Cells from Chinese Rhesus Macaques

Dendritic cells (DCs) play a pivotal role in linking the innate immunity and acquired immunity in responses to pathogen. Non-human primates such as Chinese Rhesus Macaque (CRM) are the favorable models for preclinical study of potential therapeutic drugs,