Comparative genome mapping among Populus adenopoda, P. alba, P. deltoides, P. euramericana and P. trichocarpa

Among the genus Populus, the sections Populus (white poplar), Aigeiros Duby (black poplar) and Tacamahaca Spach contain many tree species of economical and ecological important properties. Two parental maps for the inter-specific hybrid population of Populus adenopoda × P. alba (two species of Populus section) were constructed based on SSR and SRAP markers by means of a two-way pseudo-test cross mapping strategy. The same set of SSR markers developed from the P. trichocarpa (belonging to Tacamahaca section) genome which were used to construct the maps of P. deltoides and P. euramericana (two species of Aigeiros section) was chosen to analyze the genotype of the experimental population of P. adenopoda × P. alba. Using the mapped SSR markers as allelic bridges, the alignment of the white and black poplar maps to each other and to the P. trichocarpa physical map was conducted. The alignment showed high degree of marker synteny and colinearity and the closer relationship between Aigeiros and Tacamahaca sections than that of Populus and Tacamahaca. Moreover, there was evidence for the chromosomal duplication and inter-chromosomal reorganization involving some poplar linkage groups, suggesting a complicated course of fission or fusion in one of the lineages. A poplar consensus map based on the comparisons could be constructed will be useful in practical applications including marker assisted selection.     

杨树基因组中染色体基因丰度分化及EST序列对基因覆盖度的检测(英文)

高等植物基因组中,大部分序列为非表达序列,基因序列所占的比例很小,了解基因在基因组中的分布是研究基因组结构的一个重要方面。在美国能源部资助下,一个毛果杨无性系的基因组测序已经完成并对公众发布。杨树全基因组序列的完成,为我们了解林木基因组中基因的分布提供了一个特例。在本文中,我们利用泊松分析对杨树基因组中基因在各个染色体上的密度进行了检测,结果表明杨树基因组中各条染色体的基因含量存在显著差异。杨树全基因组测序项目揭示现代杨树基因组起源于一次古全基因组复制事件(称为杨柳科基因组复制),所以杨树基因组不同染色体间存在很大的同源复制片段。但是我们的研究显示,杨树基因组中大多数高度同源的染色体上基因的密度与染色体间的同源性没有明显关系,这说明杨柳科全基因组复制事件后,各个高度同源染色体上的基因发生了流失,且基因流失的速率是不一样的。同时本文还对近九万条毛果杨EST序列进行了比对分析,结果显示这些EST序列覆盖的基因仅占杨树基因组中基因总数的16.8%左右。EST测序虽然是发现基因的一个重要手段,但小规模EST测序对基因的覆盖度很低,所以小规模EST测序的应用价值是有限的。     

Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding

Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.     

Genetic transformation: a powerful tool for dissection of adaptive traits in trees

Plant transformation and regeneration systems have become indispensable parts of gene discovery and functional characterization over the last two decades. Adoption of transformation methods in studies of plant adaptation to natural environments has been slow. This is a result of poor genomic knowledge and inefficient transformation systems for species dominating terrestrial ecosystems, and logistical difficulties in conducting field tests of genetically engineered organisms. In trees, where long generation cycles, high background polymorphism, large sizes and outcrossing systems of mating make production of near-isogenic lines and large experiments difficult, transformation is an attractive alternative for establishing direct linkages between genes and adaptively significant phenotypes. Here, we outline the capabilities, challenges, and prospects for transformation to become a significant tool for studying the ecophysiological adaptation of trees to the environment. Focusing on poplars (genus Populus) as model system, we describe how transformation-based approaches can provide insights into the genes that control adaptive traits. The availability of the poplar genome sequence, along with its large expressed sequences tag (EST) databanks, facile transformation and rapid growth, enable reverse genetic approaches to be used to test virtually any hypothesis of gene function.     

Phytoremediation of chlorpyrifos by Populus and Salix

Chlorpyrifos is one of the commonly used organophosphorus insecticides that are implicated in serious environmental and human health problems. To evaluate plant potential for uptake of chlorpyrifos, several plant species of poplar (Populus sp.) and willow (Salix sp.) were investigated. Chlorpyrifos was taken up from nutrient solution by all seven plant species. Significant amounts of chlorpyrifos accumulated in plant tissues, and roots accumulated higher concentrations of chlorpyrifos than did shoots. Chlorpyrifos did not persist in the plant tissues, suggesting further metabolism of chlorpyrifos in plant tissue. To our knowledge, this work represents the first report for phytoremediation of chlorpyrifos using poplar and willow plants.     

Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex‐linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole‐genome scans that the sex‐associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of ‘turnover’ of sex‐determination regions in animals. We performed whole‐genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex‐linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex‐associated SNPs revealed this to be an XY sex‐determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex‐determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.     

Development and annotation of perennial Triticeae ESTs and SSR markers

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/).     

Thirty-four Musa (Musaceae) expressed sequence tag-derived microsatellite markers transferred to Musella lasiocarpa

We assembled 31,308 publicly available Musa EST sequences into 21,129 unigenes; 4944 of them contained 5416 SSR motifs. In all, 238 unigenes flanking SSRs were randomly selected for primer design and then tested for amplification in Musella lasiocarpa. Seventy-eight primer pairs were found to be transferable to this species, and 49 displayed polymorphism. A set of 34 polymorphic SSR markers was analyzed in 24 individuals from four wild M. lasiocarpa populations. The mean number of alleles per locus was 3.0, ranging from 2 to 7. The observed and expected heterozygosities per marker ranged from 0.087 to 0.875 (mean 0.503) and from 0.294 to 0.788 (mean 0.544), respectively. These markers will be of practical use for genetic diversity and quantitative trait loci analysis of M. lasiocarpa.     

Homology of Melanoma-Inducing Loci in the Genus Xiphophorus

Several species of the genus Xiphophorus are polymorphic for specific pigment patterns. Some of these give rise to malignant melanoma following the appropriate crossings. For one of these pattern loci from the playfish Xiphophorus maculatus the melanoma-inducing gene has been cloned and found to encode a novel receptor tyrosine kinase, designated Xmrk. Using molecular probes from this gene in Southern blot analyses on single fish DNA preparations from 600 specimens of different populations of various species of the genus Xiphophorus and their hybrids, either with or without melanoma-predisposing pattern, it was shown that all individuals contain the Xmrk gene as a proto-oncogene. It is located on the sex chromosome. All fish that carry a melanoma-predisposing locus which has been identified by Mendelian genetics contain an additional copy of Xmrk, closely linked to a specific melanophore pattern locus on the sex chromosome. The melanoma-inducing loci of the different species and populations are homologous. The additional copy of Xmrk obviously arose by a gene-duplication event, thereby acquiring the oncogenic potential. The homology of the melanoma-inducing loci points to a similar mechanism of tumor suppression in all feral fish populations of the different species of the genus Xiphophorus.     

Species‐specific microsatellite markers to monitor gene flow between exotic poplars and their natural relatives in eastern North America

Species‐specific microsatellite markers were obtained for the unambiguous recognition of five poplar species of ecological and commercial importance to eastern North America: the native species Populus balsamifera and Populus deltoides, the exotic species Populus maximowiczii, Populus nigra, Populus trichocarpa and their interspecific hybrids. Forty‐four of 71 tested primer pairs amplified simple sequence repeat (SSR) loci for all five taxa. Six of these loci showed non‐overlapping allelic diversity between species, including fixed differences. Together, they were useful to identify unambiguously the five taxa and to validate parental contributions in a group of hybrid progeny. These markers will be invaluable to detect gene flow from plantations of exotic poplar into adjacent stands of native species and between the two potentially hybridizing native species P. balsamifera and P. deltoides.     

杨亚科植物的分类与分布

杨亚科（Populoideae）植物自然分布于热带非洲和大约从北纬19°～70°度的北半球,由胡杨属（Balsamiflua）和杨属（Populus）2个属所组成。胡杨属间断分布于赤道非洲、古地中海地区和墨西哥,包含2个组（胡杨组、墨杨组）和约3个天然种。杨属分布于欧洲、亚洲、非洲（北缘）和北美洲的广大地区,包含大叶杨亚属（Subgen．Leucoides）（大叶杨组）、杨亚属（Subgen．Populus）（青杨组、黑杨组、杨组）2个亚属和约52个天然种。拟定了杨亚科属的检索表、胡杨属组和种的检索表、杨属亚属和组的检索表以及杨属中各组种的检索表。提供了一个杨树种类目录,包括它们的正名、异名、文献引注和地理分布等。