Can the spread of agriculture in Europe be followed by tracing the spread of the weed Silene latifolia. A RAPD study

On the basis of gene frequency data of three flavone glycosylating genes, populations of the agricultural weed Silene latifolia (Caryophyllaceae) in Europe can be divided into two chemical races: an eastern and a western race. Morphological data also show a clear east-west division. When the two datasets are combined at least nine different geographical races can be distinguished using cluster analysis. Because these observations are hard to explain by selection, it has been proposed that these different races probably originated as a consequence of migration during the spread of agriculture over Europe in the past. To discriminate between selection and genetic drift many more selectively neutral easy-to-score characters are needed. In order to test whether random amplified polymorphic DNAs (RAPDs) might be suitable for this purpose, we performed a small-scale RAPD analysis on 16 geographical different populations. Using Jaccard's coefficient of similarity, we calculated genetic distances by pair-wise comparisons of both unique and shared amplification products, and a dendrogram was subsequently constructed using an unweighted pair-group method with arithmetical averages (UPGMA). On the basis of the dendrogram two clusters were discerned that clearly coincide with the aforementioned east-west division in populations. As there has been little or no artificial selection on this weed, its migration routes may be a good reflection of the different geographical routes agriculture has taken. We propose that a phylogenetic analysis of RAPD data of many more populations may provide additional information on the spread of agriculture over Europe.     

Genetic analysis of two tomato mutants affected in the regulation of iron metabolism

Iron is one of the most important micronutrients for plants. Like other organisms, plants have developed active mechanisms for the acquisition of sufficient iron from the soil. Nevertheless, very little is known about the genetic mechanisms that control the active uptake. In tomato, two spontaneously derived mutants are available, which are defective in key steps that control this process. The recessive mutationchloronerva (chln) affects a gene which controls the synthesis of the non-protein amino acid nicotianamine (NA), a key component in the iron physiology of plants. The root system of the recessive mutantfer is unable to induce any of the characteristic responses to iron deficiency and iron uptake is thus completely blocked. We present a characterization of the double mutant, showing that thefer gene is epistatic over thechln gene and thus very likely to be one of the major genetic elements controlling iron physiology in tomato. In order to gain access to these two genes at the molecular level, both mutants were precisely mapped onto the high density RFLP map of tomato. Thechln gene is located on chromosome 1 and thefer gene is on chromosome 6 of tomato. Using this high-resolution map, a chromosome walk has been started to isolate thefer gene by map-based cloning. The isolation of thefer gene will provide new insights into the molecular mechanisms of iron uptake control in plants.     

Consequences of Interspecific Competition on the Virulence and Genetic Composition of a Nucleopolyhedrovirus in Spodoptera frugiperda Larvae Parasitized by Chelonus insularis

Nucleopolyhedroviruses ( Baculoviridae ) are virulent insect pathogens that generally show a high degree of host specificity and have recognized potential as biological insecticides. Whenever viruses are applied for pest control, a proportion of the infected insects will also be parasitized by hymenopteran or dipteran parasitoids and interspecific competition for host resources will occur; the severity of such competition is likely to be modulated to a large degree by the virulence of each type of parasite. We examined the impact of parasitism by the solitary egg-larval endoparasitoid Chelonus insularis (Hymenoptera: Braconidae) on the speed of kill of nucleopolyhedrovirus-infected Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae and the pattern of host growth and virus production in infected and/or parasitized hosts. We also examined the effect of parasitism on the virulence, infectivity and genetic composition of serially passaged virus. Both parasitism and viral infection resulted in a marked reduction in host growth. When third instar larvae were dually parasitized and virus-infected, the growth rate was even more severely affected compared to parasitized larvae. There was a significant increase in virus production in larvae infected at later instars. Interspecific competition resulted in a substantial decrease in pathogen production in parasitized larvae infected at the fourth instar, but not in parasitized larvae infected at earlier instars. The serial passage experiment resulted in the appearance of four distinct genetic isolates of the virus detected by restriction endonuclease analysis. Of the three isolates that appeared in nonparasitized larvae, two showed increased virulence, expressed by mean time to death, and for one of these the infectivity, expressed as LC 50 , was reduced. One isolate that appeared in parasitized larvae (isolate D) had increased virulence and infectivity. Southern blot analysis indicated that virus isolate D was most likely generated by point mutation of a restriction site or by alterations such as duplications, deletions or by recombination of two or more genotypic variants present in the wild-type nucleopolyhedrovirus isolate. Our study provides clear evidence of interspecific competition within the host, since, depending on the timing of inoculation, adverse effects were observed upon both the parasitoid and the virus.     

Searching for a needle in the haystack: comparing six methods to evaluate heteroplasmy in difficult sequence context

Mitochondrial DNA (mtDNA) mutations have been involved in disease, aging and cancer and furthermore exploited for evolutionary and forensic investigation. When investigating mtDNA mutations the peculiar aspects of mitochondrial genetics, such as heteroplasmy and threshold effect, require suitable approaches which must be sensitive enough to detect low-level heteroplasmy and, precise enough to quantify the exact mutational load. In order to establish the optimal approach for the evaluation of heteroplasmy, six methods were experimentally compared for their capacity to reveal and quantify mtDNA variants. Drawbacks and advantages of cloning, Fluorescent PCR (F-PCR), denaturing High Performance Liquid Chromatography (dHPLC), quantitative Real-Time PCR (qRTPCR), High Resolution Melting (HRM) and 454 pyrosequencing were determined. In particular, detection and quantification of a mutation in a difficult sequence context were investigated, through analysis of an insertion in a homopolymeric stretch (m.3571insC).     

同名小麦地方品种小红芒和小红芒麦形态学和HMW-GS组成的演变分析

为了研究来自不同麦区的61份同名小麦地方品种小红芒和6份小红芒麦的遗传演变趋势,对与6个产量相关的农艺性状和高分子量麦谷蛋白亚基(high molecular weight glutenin subunits,HMW-GS)组成的变异进行了分析.结果表明,无论是在形态学水平还是蛋白质水平,小红芒和小红芒麦均存在丰富的遗传变异.在形态学水平上,供试材料的变异系数在株高、稳长、有效分蘖数、小穗数、穗粒数和千粒重等农艺性状上的变化范围分别为0.03～0.11、0.06～0.22、0.20～0.65、0.04～0.18、0.14～0.44和0.05～0.29.通过形态学数据计算小红芒和小红芒麦品种内多样性指数和品种间多样性指数,发现前者(0.804)占总多样性指数(0.842)的95.5%,而后者仅占4.5%,可见形态学变异主要来源于品种内而非品种闻,说明这些同名材料是由一个品种演变而来.在HMW-GS组成上,共发现了20种亚基组合类型,其中null,7+8,2+12和null,7+8,2+102种亚基组合出现的频率最高,分别为64.48%和20.00%.比较不同麦区种植的小红芒和小红芒麦的遗传多样性水平,发现无论是在形态学水平还是在蛋白质水平,春麦区材料的遗传多样性均普遍高于冬麦区,并且来自西北春麦区和北部春麦区的材料不仅遗传多样性较高,而且变异来源丰富,其中来自西北春麦区的甘肃天祝一带材料多样性最高,且其所处地理位置便于农作物的传播,故甘肃天祝地区有可能是小红芒的最初种植地点,然后再引种到其他种植区.     

Allozyme diversity in pheasants (<Emphasis Type="Italic">Phasianus</Emphasis> spp.) from breeding stations in Serbia

The pheasant breeds are widely used for restocking of natural populations depleted by hunting. The pheasant population number decline was detected during the 1970s in many hunting areas of Europe. One of its possible reasons might be the loss of adaptability in populations originating from breeding stations, which was caused by inbreeding depression. The aim of this paper was the analysis of genetic variability in pheasant populations from three breeding stations in Vojvodina province (Serbia) by means of allozyme diversity detection. The allozyme variability analysis of pheasants from all three breeding stations revealed polymorphisms at nine loci: Ldh-1, Mor-1, Mor-2, Es-1, Mod-2, Pgd, Gpi-2, Odh, and Sod. The analysis of individuals from three different breeding stations showed mean values of observed heterozygosity of H _o=0.137, polymorphism P _95%=30%, and H/P ratio H/P=0.430, which indicate a normal level of genetic variability for bird populations. Comparative analysis of three pheasant populations showed a high level of interpopulation differentiation.     

Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

Präadaptation, Wirtskreiserweiterung and Parallel-Cladogenese in der Evolution von phytophagen Insekten1, 2

Preadaptation, host shifts and parallel cladogenesis in the evolution of phytophagous insects In this contribution we investigate the possibilities to apply concepts developed for the evolution of animal parasites to insect-plant systems. We compare host parasite systems in animals with plant-herbivore systems and list similarities and differences. The terms preadaptation, predisposition, expansion and contraction of host ranges, and parallel cladogenesis are discussed. We enumerate general preadaptations for the evolution of herbivory in insects and preadaptations for shifts between herbivory and entomophagy. Examples are given for expansions of host ranges based on phytochemical or structural characters of host plants. Cases of parallel cladogenesis in herbivoreparasitoid systems and plant-herbivore systems are compiled from the literature. An analysis of the insect fauna of the “thistles” (Cynaroideae) in the Palearctic and Nearctic demonstrates the importance of the evolutionary history of the plant taxa and of the existence of preadapted pools of herbivores for the evolution of guilds of specialized herbivores. The members of the Curculionid taxon Cleoninae provide examples for multiple colonizations and radiations of herbivores on the Cynaroideae. The taxonomic and biological relationships of the weevil genera Rhinocyllus, Bangasternus and Larinus which exploit the flower heads of Cynaroideae, can be interpreted as result of a basic parallel cladogenesis between herbivore and host. A gelelectrophoretic analysis of Larinus spp. supports this hypothesis.     

Rooting strategy of naturally regenerated beech in Silver birch and Scots pine woodlands

This study investigated the belowground development and strategy of late-successional European beech (Fagus sylvatica L.) in ageing natural Scots pine (Pinus sylvestris L.) and Silver birch (Betula pendula Roth.) woodlands in a French volcanic mid-elevation area. For this purpose root biomass, root profile and fine-root architecture of competitor trees were examined in 53 mixed pine–beech and 42 birch–beech woodlands along a stand maturation gradient, using the root auger technique (0–75-cm). The total beech fine-root biomass highly correlated with aerial dimensions such as stem height and girth, whereas it moderately correlated with its age, thus indicating the effects of competition. Basic stand biometric data such as stand density and basal area had no significant effect on beech root biomass. Conversely, competition indices taking into account the vertical dimensions of competitor trees were efficient, probably due to redundancy with beech height. At similar age and height, beeches under birch had a greater belowground development than beeches under pine. Each species exhibited specific rooting pattern and plasticity of fine-root architecture along the gradients of stand maturation and competition. Beech had a heart-shaped rooting habit in both mixings, which strongly increased along stand maturation. Its fine-root system adopted a foraging strategy to respond to increasing stand competition. The Scots pine fine-root system was plate-like and showed a low morphological plasticity, thus presumably a conservative strategy. Silver birch exhibited a high biomass and a foraging capacity in the topsoil but a loose root system in the subsoil. The coexistence of pine and beech roots in the upper soil presumably leads to a high belowground competition. Beech root system becomes predominant throughout the soil profile and it adopts an efficient foraging strategy, but at the expense of its belowground development. Conversely, the niche partitioning strategy between beech and birch may explain why beech develops strongly belowground in spite of the fact that birch has a dense rooting and a competitive fine-root architecture. As a consequence, beech mid-term regeneration and development may be facilitated under birch as compared with pine.     

Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop

Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 ± 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [F_st(theta) = 0.091 ± 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation.Communicated by H.C. Becker