Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations.     

板栗群体的遗传多样性及人工选择的影响

利用水平板淀粉凝胶电泳技术对板栗９个群体１１个种同工酶系统的１２个酶位点进行分析,结果表明板栗（Ｃａｓｔａｎｅａｍｏｌｉｓｉｎａ）为多态性物种,遗传变异水平较高,其多态位百分率为７１．３％,每个位点的等位基因平均数为２．２７,平均期望杂合值为０．３４６;总的基因多样性中,８９．３％发生于群体内,各群体之间的遗传距离为０．０１０～０．１７７;对各等位基因频率进行ＰＣＡ分析,筛选出较合适的基因标记位点及构建了板栗遗传结构的空间变异模式。在综合前人研究的基础上,初步探讨了人工选择对板栗遗传多样性的影响,初步推测出西南为板栗遗传多样性中心     

Genetic Diversity and Natural Selection of the Plasmodium knowlesi Circumsporozoite Protein Nonrepeat Regions

Background

Plasmodium knowlesi is a simian malaria parasite that has been identified to cause malaria in humans. To date, several thousand cases of human knowlesi malaria have been reported around Southeast Asia. Thus far, there is no detailed study on genetic diversity and natural selection of P. knowlesi circumsporozoite protein (CSP), a prominent surface antigen on the sporozoite of the parasite. In the present study, the genetic diversity and natural selection acting on the nonrepeat regions of the gene encoding P. knowlesi CSP were investigated, focusing on the T-cell epitope regions at the C-terminal of the protein.

Methods

Blood samples from 32 knowlesi malaria patients and 2 wild monkeys (Macaca fascicularis) were used. The CSP of the P. knowlesi isolates was amplified by PCR, cloned into Escherichia coli, and sequenced. The nonrepeat regions of the CSP gene were analysed for genetic diversity, natural selection and haplotypic grouping using MEGA5 and DnaSP version 5.10.00 programmes. A haplotype network was constructed based on the C-terminal (Th2R/Th3R) T-cell epitope regions using the Median-Joining method in the NETWORK version 4.6.1.2 programme. Previously published sequences from other regions (Malaysia Borneo, Singapore) were also included in the analysis.

Results

A total of 123 P. knowlesi CSP sequences were analysed. Multiple sequence alignment revealed 58 amino acid changes, and 42 novel amino acid haplotypes were identified. Polymorphism was higher in the C-terminal Th2R/Th3R epitope (π = 0.0293, n = 123) region compared to the overall combined nonrepeat regions (π = 0.0120, n = 123). Negative natural selection was observed within the nonrepeat regions of the CSP gene. Within the C-terminal Th2R/Th3R epitope regions, there was evidence of slight positive selection. Based on haplotype network analysis of the Th2R/Th3R regions, five abundant haplotypes were identified. Sharing of haplotypes between humans and macaques were observed.

Conclusion

This study contributes to the understanding of the type and distribution of naturally occurring polymorphism in the P. knowlesi CSP gene. This study also provides a measurement of the genetic diversity of P. knowlesi and identifies the predominant haplotypes within Malaysia based on the C-terminal Th2R/Th3R regions.     

利用SSR标记分析玉米轮回选择群体的遗传多样性

利用SSR标记技术分析了玉米基础群体DC0及其选择两轮后的群体HSC2和MSC2以及基础群体XFC0和其选择一轮后的群体XFC1的遗传多样性。结果表明：49对引物在5个玉米群体中共扩增出185个等位位点,每个SSR座位的等位基因数目为1～7个,平均为3．8个;基础群体多态性位点总数和多态性位点比例比其改良群体的略高;DC0、HSC2和MSC2 3个群体的基因平均杂合度相似,XFC0与XFC1的基因平均杂合度相似;基础群体与改良群体的平均遗传距离也相似;累加各引物扩增的基因型种类,改良群体的基因型种类偏少,但这些差异均不显著。以上结果说明轮回选择的基础群体与其改良后群体的遗传变异相似,轮回选择可以保持群体的遗传变异范围,改变群体的遗传组成,增加群体内个体间的异质性。     

Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

Genetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing, we find that static environments are uniquely characterized by a small number of high-fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short-term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.     

Modeling Interference in Genetic Recombination

In analyzing genetic linkage data it is common to assume that the locations of crossovers along a chromosome follow a Poisson process, whereas it has long been known that this assumption does not fit the data. In many organisms it appears that the presence of a crossover inhibits the formation of another nearby, a phenomenon known as ``interference.' We discuss several point process models for recombination that incorporate position interference but assume no chromatid interference. Using stochastic simulation, we are able to fit the models to a multilocus Drosophila dataset by the method of maximum likelihood. We find that some biologically inspired point process models incorporating one or two additional parameters provide a dramatically better fit to the data than the usual ``no-interference' Poisson model.     

The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations

It is well known that most new mutations that affect fitness exert deleterious effects and that natural populations are often composed of subpopulations (demes) connected by gene flow. To gain a better understanding of the joint effects of purifying selection and population structure, we focus on a scenario where an ancestral population splits into multiple demes and study neutral diversity patterns in regions linked to selected sites. In the background selection regime of strong selection, we first derive analytic equations for pairwise coalescent times and F_ST as a function of time after the ancestral population splits into two demes and then construct a flexible coalescent simulator that can generate samples under complex models such as those involving multiple demes or nonconservative migration. We have carried out extensive forward simulations to show that the new methods can accurately predict diversity patterns both in the nonequilibrium phase following the split of the ancestral population and in the equilibrium between mutation, migration, drift, and selection. In the interference selection regime of many tightly linked selected sites, forward simulations provide evidence that neutral diversity patterns obtained from both the nonequilibrium and equilibrium phases may be virtually indistinguishable for models that have identical variance in fitness, but are nonetheless different with respect to the number of selected sites and the strength of purifying selection. This equivalence in neutral diversity patterns suggests that data collected from subdivided populations may have limited power for differentiating among the selective pressures to which closely linked selected sites are subject.     

Alteration of Sexual Reproduction and Genetic Diversity in the Kelp Species Laminaria digitata at the Southern Limit of Its Range

Adaptation to marginal habitats at species range-limits has often been associated with parthenogenetic reproduction in terrestrial animals and plants. Laboratory observations have shown that brown algae exhibit a high propensity for parthenogenesis by various mechanisms. The kelp Laminaria digitata is an important component of the ecosystem in Northern European rocky intertidal habitats. We studied four L. digitata populations for the effects of marginality on genetic diversity and sexual reproduction. Two populations were marginal: One (Locquirec, in Northern Brittany) was well within the geographic range, but was genetically isolated from other populations by large stretches of sandy beaches. Another population was at the range limits of the species (Quiberon, in Southern Brittany) and was exposed to much higher seasonal temperature changes. Microsatellite analyses confirmed that these populations showed decreased genetic and allelic diversity, consistent with marginality and genetic isolation. Sporophytes from both marginal populations showed greatly diminished spore-production compared to central populations, but only the southern-limit population (Quiberon) showed a high propensity for producing unreduced (2N) spores. Unreduced 2N spores formed phenotypically normal gametophytes with nuclear area consistent with ≥2N DNA contents, and microsatellite studies suggested these were produced at least in part by automixis. However, despite this being the dominant path of spore production in Quiberon sporophyte individuals, the genetic evidence indicated the population was maintained mostly by sexual reproduction. Thus, although spore production and development showed the expected tendency of geographical parthenogenesis in marginal populations, this appeared to be a consequence of maladaptation, rather than an adaptation to, life in a marginal habitat.     

Unexpected High Genetic Diversity at the Extreme Northern Geographic Limit of Taurulus bubalis (Euphrasen, 1786)

The longspined bullhead (Taurulus bubalis, Euphrasen 1786) belongs to the family Cottidae and is a rocky shore species that inhabits the intertidal zones of the Eastern Atlantic since Iceland, southward to Portugal and also the North Sea and Baltic, northward to the Gulf of Finland, with some occurrences in the northern Mediterranean coasts eastward to the Gulf of Genoa. We analysed the phylogeographic patterns of this species using mitochondrial and nuclear markers in populations throughout most of its distributional range in west Europe. We found that T. bubalis has a relatively shallow genealogy with some differentiation between Atlantic and North Sea. Genetic diversity was homogeneous across all populations studied. The possibility of a glacial refugium near the North Sea is discussed. In many, but not all, marine temperate organisms, patterns of diversity are similar across the species range. If this phenomenon proves to be most common in cold adapted species, it may reflect the availability of glacial refugia not far from their present-day northern limits.     

Genetic Diversity in Frontotemporal Dementia

Molecular Biology - Frontotemporal dementia is a progressive neurodegenerative disorder with high clinical, genetic, and pathomorphological diversity It is the third most common cause of dementia...     

藏鸡群体遗传多样性研究

藏鸡的体型外貌和生活习性与红色原鸡非常相似,是具有自己独特群体遗传特性的高原地方鸡种。为了有效保护并合理利用这一遗传资源,我们采用多重PCR与半自动荧光标记微卫星聚丙烯酰胺凝胶电泳相结合的方法检测了20个微卫星基因座的多态性,并随机抽取藏鸡群体中部分个体进行个体体形特征与生产性能的统计。结果表明藏鸡群体的20个微卫星基因座的多态等位基因数为4~10个,平均值为7.25个/基因座,多态信息含量（CPI）和杂合度（H）平均值分别为0.67、0.74。大染色体较小染色体的微卫星标记多态性程度要高。藏鸡群体的微卫星基因座多态性丰富,也解释了生产性能不均,外貌表现迥异的群体遗传特性。 Abstract: Morphological traits and living habit of Tibetan chicken, which is an aboriginal chicken breed on plateau with its own characteristic populational genetic features, are in great common with the Red Jungle Fowl, the assumed ancestry of domestic chicken. To fully exploit this chicken resource, Multiplex PCR with semi-automated polyacrilamide gel electrophoresis (PAGE) using fluorescently labeled microsatellite primers was used to detect the polymorphism at 20 microsatellite loci. At the same time, we randomly test the individual morphology and performance. It showed that numbers of polymorphic alleles were 4-10, with mean value 7.25 per locus. Polymorphism Information Content (CPI) and Heterozygosity (H) had mean values 0.67 and 0.74, respectively. Macrochromosomes had relatively higher polymorphism than microchromosomes(P>0.05). In all, high polymorphisms at microsatellite loci related to the uneven production performance and morphological discrepancy of population genetic characteristics in Tibetan chicken.     

Genetic Diversity and Lack of Artemisinin Selection Signature on the Plasmodium falciparum ATP6 in the Greater Mekong Subregion

The recent detection of clinical Artemisinin (ART) resistance manifested as delayed parasite clearance in the Cambodia-Thailand border area raises a serious concern. The mechanism of ART resistance is not clear; but the P. falciparum sarco/endoplasmic reticulum Ca²⁺-ATPase (PfSERCA or PfATP6) has been speculated to be the target of ARTs and thus a potential marker for ART resistance. Here we amplified and sequenced pfatp6 gene (∼3.6 Kb) in 213 samples collected after 2005 from the Greater Mekong Subregion, where ART drugs have been used extensively in the past. A total of 24 single nucleotide polymorphisms (SNPs), including 8 newly found in this study and 13 nonsynonymous, were identified. However, these mutations were either uncommon or also present in other geographical regions with limited ART use. None of the mutations were suggestive of directional selection by ARTs. We further analyzed pfatp6 from a worldwide collection of 862 P. falciparum isolates in 19 populations from Asia, Africa, South America and Oceania, which include samples from regions prior to and after deployments ART drugs. A total of 71 SNPs were identified, resulting in 106 nucleotide haplotypes. Similarly, many of the mutations were continent-specific and present at frequencies below 5%. The most predominant and perhaps the ancestral haplotype occurred in 441 samples and was present in 16 populations from Asia, Africa, and Oceania. The 3D7 haplotype found in 54 samples was the second most common haplotype and present in nine populations from all four continents. Assessment of the selection strength on pfatp6 in the 19 parasite populations found that pfatp6 in most of these populations was under purifying selection with an average d_N/d_S ratio of 0.333. Molecular evolution analyses did not detect significant departures from neutrality in pfatp6 for most populations, challenging the suitability of this gene as a marker for monitoring ART resistance.     

逆转座子与生物遗传多样性

生物为了适应环境变化,需要遗传物质发生变化来为进化提供材料,在进化过程中遗传物质的变化方式主要包括突变和基因重排。对一个种群或个体来讲,在不同的环境或一定生活周期内的不同阶段,基因组存在着基因的差次表达,这种调控在核酸分子水平上主要是通过突变的基因重排水平实现,由此使得基因组成为一个动态变化的体系,使种群或个体的遗传多样性发生相应的变化。分子生物学中最惊人的发现之一是在基因组内存在着通过DNA转录为RNA后,再经逆转录成为cDNA并插入到基因组的新位点上的因子,被称为逆转座子。按照其结构特点以及所编码反转录蛋白因子的不同,可分为反转录转位因子,反转录子,反转录病毒,能编码反转录所需蛋白的因子,不能编码反转录所需蛋白的因子。逆转座子在转位过程中须以RNA作为中间体,RNA较易变异,且RNA聚合酶和逆转录酶均无校对功能,这就使得逆转座子具有高度变异性。逆转座子可通过遗传变异,基因重排或对基因表达的影响,导致生物遗传多样性的形成。逆转座子除了能够促进基因的流动性增加遗传多样性外,它们散布在基因组中,还能够成为进化的种子。     

Serpentine Soils Do Not Limit Mycorrhizal Fungal Diversity

Background

Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants; however, their effect on other organisms is still poorly understood.

Methodology/Principal Findings

We used a combination of field and molecular approaches to test the hypothesis that serpentine fungal communities are species-poor and specialized. We conducted surveys of ectomycorrhizal fungal diversity from adjacent serpentine and non-serpentine sites, described fungal communities using nrDNA Internal Transcribed Spacer (ITS) fragment and sequence analyses, and compared their phylogenetic community structure. Although we detected low fungal overlap across the two habitats, we found serpentine soils to support rich fungal communities that include representatives from all major fungal lineages. We failed to detect the phylogenetic signature of endemic clades that would result from specialization and adaptive radiation within this habitat.

Conclusions/Significance

Our results indicate that serpentine soils do not constitute an extreme environment for ectomycorrhizal fungi, and raise important questions about the role of symbioses in edaphic tolerance and the maintenance of biodiversity.     

福建省放线菌结瘤植物共生菌Frankia遗传多样性研究

[目的]了解福建省放线菌结瘤植物共生固氮菌Frankia的遗传多样性.[方法]利用16S-23SrDNA间隔区(rrn)和nifD-K基因间隔区的PCR扩增和RFLP技术,分析了福建省木麻黄、杨梅、桤木、胡颓子等共生Frankia纯培养菌株的遗传差异.[结果]17个菌株获得rrn扩增片段,2个杨梅菌株和1个胡颓子菌株扩增未成功,酶切图谱经聚类分析表明6个地点的细枝木麻黄、短枝木麻黄、粗枝木麻黄12个共生Frankia菌株同源性高,属于一个类群,2个地点的4个杨梅菌株和1个四川桤木菌株亲缘关系近,为另一类群.25个Frankia菌株的,nifD-K基因间隔区PCR-RFLP分析结果显示,7个地点的3种木麻黄14个菌株聚类为一个类群,4个地点的7个杨梅菌株、2个地点的2个四川桤木菌株以及1个台湾桤木菌株聚类为另一个类群,胡颓子菌株则为独立的类群.[结论]研究结果表明福建省共生Frankia遗传多样性丰富.     

松属植物遗传多样性研究进展

研究松属遗传多样性的方法涉及表型、同工酶、染色体、DNA等多层面。 松树表型性状变异广泛,其不同树种不同性状的遗传力（或遗传率）均存在差异。到目前为止,同工酶仍是检测松树遗传多样性的最常用方法,一般而言,松属树种群体内等位酶多样性程度高,群体间分化较低,但各树种的情形也不尽相同。松属树种染色体水平的变异很低,其核型高度一致。核DNA组较一般阔叶树大,遗传多样性丰富,但叶绿体等质体DNA则多样性较低。影响遗传多样性的因素很多,其中自身的交配系统和外部的生长环境是影响它的两个主要因素。最后,回顾了松树的起源及其遗传多样性保护策略等方面的研究。 Abstract:The ways of probing genetic diversity of pines involve many aspects,such as morphology,chromosome,isozyme,DNA,etc.The phenotypic characteristics in pines vary widely and the differences of inheritability(h2) are obvious among characteristics and among species.Up to now,isozyme is still the most common means to measure genetic diversity of pines.Generally,there are high allozyme diversity within populations and low differentiation coefficient among populations,but differences exist between species in Pinus.The variations of chromosome among pines are very low and the karyotypes of pines are consentaneous,but the genomes of pines in cell nucleus are much larger than that of broadleaves.Diversity of pines are abundant at nucleus DNA level but are poor at plastid DNA level,such as ctDNA.There are many factors that will affect genetic diversity of pines,in which mating system and environment are two main factors.Finally,we reviewed the research on origin of Pinus and conservation strategy of genetic diversity,etc.     

Modulation of Flavivirus Population Diversity by RNA Interference

To test the hypothesis that RNA interference (RNAi) imposes diversifying selection on RNA virus genomes, we quantified West Nile virus (WNV) quasispecies diversity after passage in Drosophila cells in which RNAi was left intact, depleted, or stimulated against WNV. As predicted, WNV diversity was significantly lower in RNAi-depleted cells and significantly greater in RNAi-stimulated cells relative to that in controls. These findings reveal that an innate immune defense can shape viral population structure.     

Genetic Diversity and the Survival of Populations

Abstract: In this comprehensive review, a range of factors is considered that may influence the significance of genetic diversity for the survival of a population. Genetic variation is essential for the adaptability of a population in which quantitatively inherited, fitness-related traits are crucial. Therefore, the relationship between genetic diversity and fitness should be studied in order to make predictions on the importance of genetic diversity for a specific population. The level of genetic diversity found in a population highly depends on the mating system, the evolutionary history of a species and the population history (the latter is usually unknown), and on the level of environmental heterogeneity. An accurate estimation of fitness remains complex, despite the availability of a range of direct and indirect fitness parameters. There is no general relationship between genetic diversity and various fitness components. However, if a lower level of heterozygosity represents an increased level of inbreeding, a reduction in fitness can be expected. Molecular markers can be used to study adaptability or fitness, provided that they represent a quantitative trait locus (QTL) or are themselves functional genes involved in these processes. Next to a genetic response of a population to environmental change, phenotypic plasticity in a genotype can affect fitness. The relative importance of plasticity to genetic diversity depends on the species and population under study and on the environmental conditions. The possibilities for application of current knowledge on genetic diversity and population survival for the management of natural populations are discussed.     

东南亚国家引进水稻种质的遗传多样性和遗传结构分析

用72对SSR引物对316份东南亚不同地理来源的水稻种质资源进行遗传多样性和遗传结构分析。结果表明,共检测到387个等位基因,平均每对引物检测到5.375个,变幅在2~12之间;其中频率5%的稀有等位基因有293个,占全部等位基因数的75.7%。Nei基因多样性指数(He)变化幅度在0.055~0.855之间,平均为0.623。He以菲律宾的种质资源最为丰富(He=0.619),其余国家的He大小依次是越南(He=0.515)老挝(He=0.467)柬埔寨(He=0.455);聚类分析显示分为籼粳稻两大群体,地理分组不是特别清晰。AMOVA分析表明,遗传变异主要来源于不同地理类群间,且遗传分化极显著。遗传结构分析结果显示K=2时,有相对明显的遗传结构。其次是K=5时,显示菲律宾群体分为了3个比较明显的小类群,存在较为明显的遗传分化结构。东南亚引进水稻种质资源丰富的遗传多样性和遗传结构为后期水稻育种的亲本选择提供依据。