Isolation of novel microsatellite markers for the clouded Apollo (P. mnemosyne Linnaeus, 1758; Lepidoptera,Papilionidae)

Five novel polymorphic microsatellite loci were isolated and characterized using an enriched genomic DNA library for Parnassius mnemosyne, a European butterfly of conservation concern, and a valuable model for the study of metapopulation dynamics. Allele numbers ranged from 4 to 12 and observed and expected heterozygosities from 0.17 to 0.74 and from 0.26 to 0.835, respectively. Two samples from geographically close populations were analyzed, demonstrating that the new markers can be successfully employed to investigate fine-scale population structure.     

Nitric oxide donor-mediated inhibition of phosphorylation shows that light-mediated degradation of photosystem II D1 protein and phosphorylation are not tightly linked

An outcome of the photochemistry during oxygenic photosynthesis is the rapid turn over of the D1 protein in the light compared to the other proteins of the photosystem II (PS II) reaction center. D1 is a major factor of PS II instability and its replacement a primary event of the PS II repair cycle. D1 also undergoes redox-dependent phosphorylation prior to its degradation. Although it has been suggested that phosphorylation modulates D1 metabolism, reversible D1 phosphorylation was reported not to be essential for PS II repair in Arabidopsis. Thus, the involvement of phosphorylation in D1 degradation is controversial. We show here that nitric oxide donors inhibit in vivo phosphorylation of the D1 protein in Spirodela without inhibiting degradation of the protein. Thus, D1 phosphorylation is not tightly linked to D1 degradation in the intact plant.     

Development and characterization of simple sequence repeat (SSR) markers in the water lotus (Nelumbo nucifera)

Simple sequence repeat (SSR) markers were developed in the water lotus (Nelumbo nucifera Gaertn.) from an SSR-enriched genomic library. Of the SSR markers tested, 11 primer pairs produced clearly distinguishable DNA banding patterns. Forty-three alleles were detected with the 11 markers. The allele number per locus ranged from 2 to 5 with an average of 3.9. Polymorphism values ranged from 0.11 to 0.66 with an average of 0.51. These primers were also applicable to another Nelumbo species, Nelumbo lutea (Willd.) Pers. (American lotus) and hybrids between N. nucifera and N. lutea. These results indicate that the SSR markers developed in this study are informative and will be useful for genetic analysis in Nelumbo species.     

Genetic variation and control of chloroplast pigment concentrations and related needle-level traits in Picea rubens, Picea mariana, and their hybrids: moisture and light environmental effects

Chlorophyll pigment concentrations and proportions, nitrogen (N), and needle morphology traits, are important components of growth and were examined in five hybrid index categories from controlled crosses of various crosstypes, ranging from pure black spruce (BS) [Picea mariana (Mill.) B.S.P.] to pure red spruce (RS) (Picea rubens Sarg.) grown under controlled light and water environments. Black spruce had on average 10% greater total chlorophyll concentration (CHL) than RS. Red spruce had proportionately less chlorophyll a:b and CHL:CAR (carotenoid) ratios than BS. Nitrogen (N) concentrations were 1.75 and 1.60% for BS and RS, respectively. Black spruce had the lowest carbon (C):N ratio (29.7) and RS had among the highest (32.3). Interestingly, there was no difference in specific needle area among hybrid indices. Most of the chlorophyll pigment, C and N traits followed an additive inheritance model, evidenced by a near-linear relationship from BS to RS across hybrid indices. However, for CHL, CAR, and CHL:CAR ratio, parental analysis showed significant male effects and non-significant female and male × female interaction effects. Black spruce males had 15.1 and 9.6% higher CHL and CAR, respectively, than hybrid or RS males, thus showing an underlying paternally inherited genetic control. Controlling for N differences, analysis of covariance (ANCOVA) showed that sun-grown seedlings had 22.2% or 300 μg g⁻¹ lower CHL than shade-grown seedlings. Controlling for N, ANCOVA showed that the drought-grown seedlings actually had 6.7% or 100 μg g⁻¹ greater CHL than the irrigated seedlings. Sun plus drought conditions gave the lowest CHL, N, and CHL:CAR ratio of all treatments, showing an additive multi-stress effect. There was a significant hybrid index × light effect as a result of rank changes. Sun-grown RS had the lowest CHL and N values, whereas shade-grown RS had among the highest CHL and N values. Red spruce are at a competitive disadvantage compared with BS and most hybrid spruce in high light, high drought, and high light plus drought conditions. Red spruce will be strongly limited in its distribution by successional opportunities resulting from prevalent harvesting practices such as clearcutting. Silvicultural modifications and genetic restoration will be required to maintain RS on the landscape of northeastern North America.     

亚历山大藻属微卫星标记的筛选

采用生物信息学方法,从塔玛亚历山大藻的ESTs数据库中筛选微卫星(Simple Sequence Repeat, SSR)位点,设计SSR引物,利用毛细管电泳对4株塔玛亚历山大藻(Alexandrium tamarense)、2株相关亚历山大藻(Alexandrium affine)和1株链状亚历山大藻(Alexandrium catenella)进行种内、种间遗传多样性分析,获得以下主要结果:(1)从6830条非冗余的ESTs中共查找到222个SSR,平均每18.5kb就有一个SSR,三核苷酸重复在所有的重复类型中所占比例最大,达到48.2%,重复单元CTG/CAG出现频率最高.进一步筛选出12条SSR引物,用于遗传多样性分析.(2)种内遗传多样性水平整体偏低,多态性引物比率仅为41 67%,Nei's基因多样性平均为0.2130.种间遗传多样性水平较高,多态性引物比率为75%,Nei's基因多样性平均水平为0 4643;另外,种间遗传分化系数较高,平均水平为0.7051.(3)对7个样品的聚类图分析发现,A. tamarense CCMP116 与A. affine CCMP112遗传距离极为接近;A. tamarense ATHK9301、CCMP1598和ATDH01相互聚在一起;A. catenella ACDH01与A. tamarense分属两枝.以上结果表明,SSR标记在亚历山大藻种内遗传多样性分析方面是一种非常有用的工具.     

Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of <Emphasis Type="Italic">Amborella</Emphasis> and <Emphasis Type="Italic">Ceratophyllum</Emphasis>

It is widely appreciated that noisy, highly variable data can impede phylogeney reconstruction. Researchers have for a long time omitted problematic data from phylogenetic analyses, such as the third-codon positions and variable regions. In the analyses of the phylogenetic relations of the angiosperms; however, inclusion of complete gene sequences into genomic-scale alignments has become a common practice. Here we demonstrate that this practice can be misleading. We show that support of the basal-most position of Amborella trichopoda among the angiosperms in the chloroplast genomic data is based only on a tiny subset (< 1% of the total alignment length) of the most variable positions in alignment, exhibiting mean maximum likelihood (ML) distance among the angiosperm operational taxonomic units (OTUs) approximately 36 substitutions/site. Exclusion of these positions leads to disappearance of the basal Amborella branch. Likewise, the recently reported sister-group relationship of Ceratophyllum to the eudicots is based on the presence of 2% of the most variable positions in the genomic alignment, exhibiting, on average, 20 substitutions/site in comparison among the angiosperm OTUs. These observations highlight a need for excluding a certain proportion of saturated positions in alignment from phylogenomic analyses.     

Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome

A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A cherry map from the inter-specific cross Prunus avium ‘Napoleon’ × P. nipponica based on microsatellite, gene-specific and isoenzyme markers

One hundred and sixty microsatellite (simple sequence repeat (SSR)) and six gene-specific markers revealing 174 loci were scored in 94 seedlings from the inter-specific cross of Prunus avium ‘Napoleon’ × Prunus nipponica accession F1292. The co-segregation data from these markers were used to construct a linkage map for cherry which spanned 680 cM over eight linkage groups with an average marker spacing of 3.9 cM per marker and just six gaps longer than 15 cM. Markers previously mapped in Prunus dulcis ‘Texas’ × Prunus persica ‘Earlygold’ allowed the cherry map to be anchored to the peach × almond map and showed the high level of synteny between the species. Eighty-four loci segregated in P. avium ‘Napoleon’ versus 159 in P. nipponica. The segregations of 32 isoenzyme loci in a subset of 47 seedlings from the progeny were scored, using polyacrylamide gel electrophoresis and/or isoelectric focusing separation followed by activity staining, and the co-segregation data were analysed along with those for 39 isoenzymes reported previously and for the 174 sequence-tagged site loci plus an additional two SSR loci. The second map incorporates 233 loci and spans 736 cM over eight linkage groups with an average marker spacing of 3.2 cM per marker and just two gaps greater than 15 cM. The microsatellite map will provide a useful tool for cherry breeding and marker-assisted selection and for synteny studies within Prunus; the gene-specific markers and isoenzymes will be useful for comparisons with maps of other rosaceous fruit crops. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.