Distribution of genetic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatellites

 Using nine chloroplast simple sequence.repeats (cpSSRs) markers, we evaluated haplotypic variation within and among natural populations of Maritime pine (Pinus pinaster Ait.) in order to shed light on the history of this species. Seven out of the nine cpSSRs analysed were polymorphic, giving a total of 24 different variants. The 24 variants combined in 34 different haplotypes. The populations which generally showed the lowest level of haplotypic diversity are those located in Portugal. The Landes (France) and Pantelleria (Italy) populations represent the two main reservoirs of haplotypic diversity. The proportion of genetic differentiation among populations, estimated using R_st, which is a measure based upon a strict stepwise mutation model, was 0.235. The high level of differentiation was also confirmed by the AMOVA analysis (Φ_ST=0.254, P<0.001). Four main groups of populations were identified on the basis of Principal Component Analysis, with the differences being statistically significant (Φ_CT=0.299, P<0.001). Based on our results the presence of refugia located in the South of Portugal, previously proposed for this species, may be excluded, and a different possible recolonization process of Maritime pine in the post-glacial period has been proposed. Populations from North Africa and France might have represented a starting point of the recolonization process of Portugal and of the Italian part of the natural range, respectively. This hypothesis seems to be confirmed by the analysis of the distribution of the pairwise differences among individuals within populations: Landes and Pantelleria populations showed a bimodal distribution, as would be expected for ancient gene pools. Received: 5 November 1997 / Accepted: 5 January 1998     

Genetic control of stem form in Pinus pinaster Ait. seedlings exposed to lateral light

 In order to compare family differences in stem form determination, seedlings of eight half-sib progenies of Pinus pinaster were exposed to three different light treatments: fixed lateral light (T1), alternate lateral light (T2), and direct sunlight (T3). From spatial coordinates of several points along the stem we computed four variables: global leaning (GL), apical leaning (APL), flexuosity index (FL) and length of the stem (LEN). Based on comparisons of the four variables, the phototropic stimulus caused different responses in stem form at the familial level. Treatment had an important effect on stem form, although the familial response to treatments was quite variable. Heritability values (h²) of the four analyzed variables showed a different pattern of variation for the three treatments, being very stable for LEN and FL, whereas h² of APL was much greater based on T1 and T2 compared to T3, and h² of GL based on T2 was much greater compared to T3 and T1. Differences in stem form were due not only to photomorphogenetic response to different light stimuli, but also to the straightening processes such as compression wood formation. The results suggest that lateral light treatments may be useful in revealing differences in efficiency of the mechanisms involved in stem form determination. Received: 1 June 1995 / Accepted: 1 April 1997     

干旱对水稻生物钟基因和干旱胁迫响应基因每日节律性变化的影响

内源生物钟的节律运动不仅调控植物的生长发育,而且在调控植物响应和适应环境过程中发挥重要的作用。为了解水稻(Oryza sativa L.)干旱胁迫响应基因和生物钟基因在干旱条件下每日表达变化情况,本文利用实时荧光定量PCR方法研究旱稻品种IRAT109在干旱胁迫下相关基因的表达变化。结果表明,干旱胁迫导致早晨生物钟基因OsPRRs、OsLHY和OsZTL1的表达量显著下降,振幅减弱;同时导致夜晚生物钟基因OsTOC1、OsGI和OsELF3整体表达量升高,振幅增强,但对OsFKF1基因影响不大。同样,大部分水稻干旱胁迫响应基因在干旱胁迫后整体表达量显著升高,但OsDST基因表达量下降;同时大部分抗逆基因周期性表达被扰乱,但OsCIPK12、OsCDPK7和OsDREB1A依然保持24 h内震荡。本研究结果表明干旱胁迫能影响生物钟元件的基因表达,这种互相影响改变了部分基因每日的震荡变化。     

Strain distribution during anchorage failure of Pinus pinaster Ait. at different ages and tree growth response to wind-induced root movement

Winching tests were carried out on 5- 13- and 17-year-old tap rooted Maritime pine (Pinus pinaster Ait.) in order to determine how the mode of anchorage failure changes throughout the life of a tree. As trees were pulled sideways, strain along the lateral roots was recorded using strain gauges attached to a strain indicator. Measurements of strain in the root system, taken during winching, provide information about root movement when loaded by wind. The mode of mechanical failure appeared to depend on tree age. The youngest trees bent over completely during winching, but did not break due to the plasticity of their trunks. The 13-year-old trees either broke at the base of the tree (due to the presence of grafting scar tissue) or at the base of the tap-root. The oldest trees broke at the base of the tap-root and sounds of roots breaking were also heard. Strain was twice as great in the trunk compared to the roots in the 5- and 13-year-old trees and was three times greater in the compression roots of 17-year–old trees compared to that in the trunk. In one 17-year-old tree, strain was found to increase at a distance of 35 cm in tension roots before decreasing again. Although the mode of failure changed with tree size, anchorage strength increased proportionally with the third power of trunk diameter, therefore another reason why failure differs with tree age must exist. In order to determine if different types of wood were being laid down in the lateral roots in response to wind loading, maturation strains, indicating the existence of mechanical stress in developing wood cells, were measured at different points along the roots. A high correlation was found between maturation strain and strain measured during winching, in roots that lay in the wind direction only. Therefore, trees appear to be able to respond to external loading stress, even at a local level within a root. This revised version was published online in June 2006 with corrections to the Cover Date.     

红花尔基樟子松优良抗旱菌树组合的筛选

为筛选红花尔基樟子松（Pinus sylvestris var.mongolica）优良抗旱菌树组合,采用樟子松林下5个优势外生菌根真菌菌株为接种体,分别对5个月龄樟子松实生苗进行人工接种,接种8个月后观察菌根侵染情况及菌根形态,并在非干旱胁迫和干旱胁迫条件下测定不同菌树组合的生长和生理生化指标。结果表明：5个乡土菌种均能成功侵染樟子松并形成典型的外生菌根;干旱胁迫下,菌根化樟子松的各项生长指标均显著高于对照（P<0.05）,且接种粘盖牛肝菌（Suillus bovinus）具有最高的菌根侵染率、苗高、地上及地下生物量和根茎比;外生菌根共生体可通过提高植物SOD活性与POD活性,同时降低MDA含量来提高樟子松对干旱的耐受力;干旱胁迫下,所有接种处理苗木的萎蔫时间较对照处理均推迟,推迟时间最长的是粘盖牛肝菌接种处理,较对照推迟96.3 h;另外,接种处理均能显著延长宿主临界致死时间,尤其是接种粘盖牛肝菌可延长113.8 h。因此,可以认为粘盖牛肝菌与樟子松是一个较为理想的抗旱菌树组合。     

Seed-protein variation in maritime pine (Pinus pinaster Ait.) revealed by two-dimensional electrophoresis: genetic determinism and construction of a linkage map

Summary Proteins from haploid megagametophytes from 18 trees were studied by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). A total of 222 seeds, an average of 12 per tree, were analysed individually. 150 protein spots appeared to segregate on the polyacrylamide gels in at least tree. Genetic interpretations were made to define the number of loci responsible for the presence versus absence, staining differences or position variation of the segregating spots. The complete covariation observed between some spots could be the result of either the separation of a single gene product into two or more constituents, very close linkage, or the action of a pleiotropic gene. Human genetics techniques were used to map the 84 putative loci detected. Sixty-five loci were organised in 17 linkage groups, whereas 19 remained unlinked.     

Genome‐wide detection of genetic loci and candidate genes for teat number and body conformation traits at birth in Chinese Sushan pigs

Body conformation at birth and teat number are economically important traits in the pig industry, as these traits are usually explored to evaluate the growth and reproductive potential of piglets. To detect genetic loci and candidate genes for these traits, we performed a GWAS on 269 pigs from a recently developed Chinese breed (Sushan) using 38  128 informative SNPs on the Affymetrix Porcine SNP 55K Array. In total, we detected one genome‐wide significant (P = 1.31e‐6) SNP for teat number on chromosome X and 15 chromosome‐wide significant SNPs for teat number, body weight, body length, chest circumference and cannon circumference at birth on chromosomes 1, 3, 4, 6, 7, 9, 10, 13, 14, 15, 17 and 18. The most significant SNP had an additive effect of 0.74 × total teat number, explaining 20% of phenotypic variance. Five significant SNPs resided in the previously reported quantitative trait loci for these traits and seven significant SNPs had a pleiotropic effect on multiple traits. Intriguingly, 12 of the genes nearest to the significant SNPs are functionally related to body conformation and teat number traits, including SPRED2, MKX, TMSB4X and ESR1. GO analysis revealed that candidate genes proximal to the significant SNPs were enriched in the G‐protein coupled receptor and steroid hormone‐mediated signaling pathway. Our findings shed light on the genetic basis of the measured traits and provide molecular markers especially for the genetic improvement of teat number in Sushan and related pigs.     

Retracted: Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice (Oryza sativa L.) under drought stress

Due to severe water resource shortage, genetics of and breeding for DT (drought tolerance) in rice (Oryza sativa L.) have become one of the hot research topics. Identification of grain yield QTLs (quantitative trait loci) directly related to the DT trait of rice can provide useful information for breeding new drought‐resistant and water‐saving rice varieties via marker‐assisted selection. A population of 105 advanced BILs (backcross introgression lines) derived from a cross between Zhenshan97B and IRAT109 in Zhenshan97B background were grown under drought stress in a field experiment and phenotypic traits were investigated. The results showed that in the target interval of RM273‐RM255 on chromosome 4, three main‐effect QTLs related to panicle length, panicle number, and spikelet number per panicle were identified (LOD [logarithm of the odds] > 2.0). The panicle length‐related QTL had two loci located in the neighboring intervals of RM17308‐RM17305 and RM17349‐RM17190, which explained 18.80% and 20.42%, respectively, of the phenotypic variation, while the panicle number‐related QTL was identified in the interval of RM1354‐RM17308, explaining 11.47% of the phenotypic variation. As far as the spikelet number per panicle‐related QTL was concerned, it was found to be located in the interval of RM17308‐RM17305, which explained 28.08% of the phenotypic variation. Using the online Plant‐GE query system, a total of 13 matched ESTs (expressed sequence tags) were found in the target region, and of the 13 ESTs, 12 had corresponding predicted genes. For instance, the two ESTs CB096766 and CA765747 were corresponded to the same predicted gene LOC_Os04g46370, while the other four ESTs, CA754286, CB000011, CX056247, and CX056240, were corresponded to the same predicted gene LOC_Os04g46390.     

Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates

For over 3 decades, the rate of replacement mutations has been assumed to be equal to, and estimated from, the rate of "strictly" neutral sequence divergence in noncoding regions and in silent-codon positions where mutations do not alter the amino acid encoded. This assumption is fundamental to estimating the fraction of harmful protein mutations and to identifying adaptive evolution at individual codons and proteins. We show that the assumption is not justifiable because a much larger fraction of codon positions is involved in hypermutable CpG dinucleotides as compared with the introns, leading to a higher expected replacement mutation rate per site in a vast majority of the genes. Consideration of this difference reveals a higher intensity of purifying natural selection than previously inferred in human genes. We also show that a much smaller number of genes are expected to be evolving with positive selection than that predicted using sequence divergence at intron and silent positions in the human genome. These patterns indicate the need for using new approaches for estimating rates of amino acid-altering mutations in order to find positively selected genes and codons in genomes that contain hypermutable CpG's.     

Contrasting patterns of genetic variation in the two sympatric geckos Gekko tawaensis and G. japonicus (Reptilia: Squamata) from western Japan,as revealed by allozyme analyses

Allozyme variation in two congeneric sympatric geckos, Gekko tawaensis and G. japonicus, from western Japan was examined. These species show similar densities and spatial arrangements of populations in this region, and their genetic structures are thus expected to have been formed under the influences of comparable geohistorical, environmental, and demographic factors. Results of the analyses, however, revealed strikingly different genetic patterns in the two species. Populations of G. tawaensis invariably showed a remarkably lowered heterozygosity (0-0.017) compared to G. japonicus (0.089-0.124). On the other hand, the genetic heterogeneity among populations is much greater in G. tawaensis (F(ST)=0.726) than in G. japonicus (F(ST)=0.101). The Mantel test failed to detect any significant correlations between log (estimated migration rate) and log (geographic distance) in either species, or between matrices of interpopulation pairwise F(ST) for the two species. These results suggest that, in each species, formation of the current genetic structure in western Japan has been chiefly influenced by stochastic factors, rather than the geohistorical architecture of this region. The high F(ST) and low heterozygosity in G. tawaensis suggest the effects of severe local fragmentation. On the other hand, the relatively low F(ST) and high heterozygosity in G. japonicus imply extensive gene flow among populations. Absence of significant correlations between the estimated migration rate and geographic distance in G. japonicus may suggest that such gene flow is promoted by human-mediated transport of this primarily house-dwelling lizard.     

Effects of two probiotic Lactobacillus strains on jejunal and cecal microbiota of broiler chicken under acute heat stress condition as revealed by molecular analysis of 16S rRNA genes

We examined the effects of probiotic Lactobacillus strains of Lactobacillus agilis JCM 1048 and Lactobacillus salivarius subsp. salicinius JCM 1230 on jejunal and cecal microbiota of broiler chicken under heat stress condition using terminal restriction fragment length polymorphism (T-RFLP) analysis. The jejunal bacterial community was limited to a few bacterial groups, mostly Lactobacillus spp. A relatively abundant and higher prevalence of Lactobacillus spp. were observed in the jejunal and cecal microbiota of the probiotic chickens compared with those of the control chickens under heat stress condition. In general, the probiotic strains did not significantly affect the abundance of L. agilis and L. salivarius in chicken intestine but clearly contributed to increasing their prevalence in the probiotic chickens. The probiotic Lactobacillus strains enriched the diversity of Lactobacillus flora in chicken jejunum and cecum by increasing the abundance and prevalence of Lactobacillus spp. inhabiting the intestine. The richness of Lactobacillus species tended to be similar among the jejunal and cecal microbiota. The bacterial community of cecum was complex and age-dependent. The major components of the cecal microbiota were clostridia and lactobacilli. The Clostridium subcluster XIVa was the most predominant group in chicken cecum. Probiotic Lactobacillus strains restored the microbial balance and maintained the natural stability of indigenous bacterial microbiota following heat stress-induced changes.     

Genetic structure and differentiation of Gentiana atuntsiensis W. W. Smith and G. striolata T. N. Ho (Gentianaceae) as revealed by ISSR markers

The Hengduan Mountains are the core region of the Himalaya hotspot, and are renowned for their high levels of endemism. Gentiana atuntsiensis and G. striolata are two closely related and morphologically similar species endemic to this region. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure within these two species, as well as the differentiation between them. An analysis of molecular variance-derived estimate demonstrated only 13.5% of genetic differentiation between the two species. Considering their adjacent distribution patterns, low genetic divergence, and clear clustering into two groups, it is hypothesized that the two species arose from a rapid and recent speciation event induced mainly by geographical isolation. A relatively high level of genetic diversity was revealed in each species (Shannon's index of diversity: H _sp = 0.324 and 0.391; H _pop = 0.225 and 0.274; for G. atuntsiensis and G. striolata , respectively). Most of the genetic variation was partitioned within populations ( Ø _ST = 0.232 and 0.226 in G. atuntsiensis and G. striolata , respectively). The large population sizes, outcrossing breeding system, and small, light seeds that disperse widely may explain the genetic structure in both species.  © 2007 The Linnean Society of London. Botanical Journal of the Linnean Society , 2007, 154 , 225–232.     

Isolation,genetic variation and expression of TIR-NBS-LRR resistance gene analogs from western white pine (<Emphasis Type="Italic">Pinus monticola </Emphasis>Dougl. ex. D. Don.)

Western white pine (Pinus monticola Dougl. ex. D. Don., WWP) shows genetic variation in disease resistance to white pine blister rust (Cronartium ribicola). Most plant disease resistance (R) genes encode proteins that belong to a superfamily with nucleotide-binding site domains (NBS) and C-terminal leucine-rich repeats (LRR). In this work a PCR strategy was used to clone R gene analogs (RGAs) from WWP using oligonucleotide primers based on the conserved sequence motifs in the NBS domain of angiosperm NBS-LRR genes. Sixty-seven NBS sequences were cloned from disease-resistant trees. BLAST searches in GenBank revealed that they shared significant identity to well-characterized R genes from angiosperms, including L and M genes from flax, the tobacco N gene and the soybean gene LM6. Sequence alignments revealed that the RGAs from WWP contained the conserved motifs identified in angiosperm NBS domains, especially those motifs specific for TIR-NBS-LRR proteins. Phylogenic analysis of plant R genes and RGAs indicated that all cloned WWP RGAs can be grouped into one major branch together with well-known R proteins carrying a TIR domain, suggesting they belong to the subfamily of TIR-NBS-LRR genes. In one phylogenic tree, WWP RGAs were further subdivided into fourteen clusters with an amino acid sequence identity threshold of 75%. cDNA cloning and RT-PCR analysis with gene-specific primers demonstrated that members of 10 of the 14 RGA classes were expressed in foliage tissues, suggesting that a large and diverse NBS-LRR gene family may be functional in conifers. These results provide evidence for the hypothesis that conifer RGAs share a common origin with R genes from angiosperms, and some of them may play important roles in defense mechanisms that confer disease resistance in western white pine. Ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) in the WWP NBS domains were greater than 1 or close to 1, indicating that diversifying selection and/or neutral selection operate on the NBS domains of the WWP RGA family.Communicated by R. Hagemann     

Contrasting levels of genetic differentiation among populations of wolverines (<Emphasis Type="Italic">Gulo gulo</Emphasis>) from northern Canada revealed by nuclear and mitochondrial loci

Habitat loss, fragmentation, overharvest, and other anthropogenic factors have resulted in population and distribution declines for North American wolverines (Gulo gulo). Currently, wolverines east of the Hudson Bay are endangered and possibly extinct, whereas the status of wolverines throughout the remaining Holarctic is vulnerable. Three previous studies using nuclear loci have detected little to no significant structuring among wolverines sampled across northern Canada. Based on these results it has been suggested that wolverines in northern Canada represent a single, panmictic population. However, as has been shown in numerous studies, in cases of female site fidelity, it is possible to have demographically autonomous populations even with male-biased gene flow. To better assess the genetic structure of wolverines in northern Canada, we examined nine microsatellite loci and DNA sequence variation from a 200 bp fragment of the mitochondrial (mtDNA) control region for 270 wolverines from nine collecting areas representing three regions of northern Canada. In agreement with previous studies, microsatellite analyses revealed a lack of significant population substructure (F _ST=0.0004). However, analysis of molecular variance, comparisons of pairwise F _ST values and nested-clade analysis of the mtDNA data revealed considerable genetic structuring among samples of wolverines from these three regions of northern Canada. These mitochondrial data provide evidence that wolverines in Canada are genetically structured due to female philopatry. The contrasting patterns of genetic differentiation based on nuclear and mitochondrial data highlight the importance of examining both nuclear and mitochondrial loci when attempting to elucidate patterns of genetic structure.     

An underground burst of diversity – a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Using both nuclear and mitochondrial sequences, we demonstrate high genetic differentiation in the genus Talpa and confirm the existence of cryptic species in the Caucasus and Anatolia, namely, T. talyschensis Vereschagin, 1945, T. ognevi Stroganov, 1948, and Talpa ex gr. levantis. Our data support four clades in the genus Talpa that showed strong geographical associations. The ‘europaea’ group includes six species from the western portion of the genus' range (T. europaea, T. occidentalis, T. romana, T. caeca, T. stankovici, and T. levantis s.l.); another three groups are distributed further east: the ‘caucasica’ group (Caucasus), the ‘davidiana’ group (eastern Anatolia and Elburz) and T. altaica (Siberia). The phylogenetic position of T. davidiana was highlighted for the first time. The order of basal branching remains controversial, which can be attributed to rapid diversification events. The molecular time estimates based on nuclear concatenation estimated the basal divergence of the crown Talpa during the latest Miocene. A putative scenario of Talpa radiation and issues of species delimitation are discussed. © 2015 The Linnean Society of London