Tree Genetics & Genomes

http://link.springer.com/journal/11295

List of Papers (Total 100)

Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers

Eighty-six almond accessions of diverse geographic origin, ranging from Central Asia to the USA, were genotyped in 15 simple sequence repeat (SSR) loci to compare genetic diversity parameters, characterize genetic differentiation, and examine factors responsible for the maintenance of genetic diversity and population structure in almond. The mean allele number was 18.86 alleles...

Using reduced representation libraries sequencing methods to identify cpDNA polymorphisms in European beech (Fagus sylvatica L)

Reduced representation genomic libraries (RRLs) are increasingly used to answer diverse questions in evolutionary biology, which remained unresolved otherwise. In the case of European beech (Fagus sylvatica L.), former applications of nuclear and chloroplast genetic markers indicated that most of the beech populations of Central, Eastern, and Northern Europe have a very...

Molecular signatures of divergence and selection in closely related pine taxa

Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at...

Analysis of microsatellite loci in tree of heaven (Ailanthus altissima (Mill.) Swingle) using SSR-GBS

Microsatellite markers are still the marker of choice for many research questions in the field of forest genetics. However, the number of available markers is often low for species that have not been studied intensively like the tree of heaven (Ailanthus altissima). During the last decade, next-generation sequencing (NGS) has offered advanced techniques for efficiently...

SNP in the Coffea arabica genome associated with coffee quality

Association analysis was performed at the whole genome level to identify loci affecting the caffeine and trigonelline content of Coffea arabica beans. DNA extracted from extreme phenotypes was bulked (high and low caffeine, and high and low trigonelline) based on biochemical analysis of the germplasm collection. Sequencing and mapping using the combined reference genomes of C...

LTR retrotransposons from the Citrus x clementina genome: characterization and application

Long terminal repeat retrotransposons (LTR-RTs) are a large portion of most plant genomes, and can be used as a powerful molecular marker system. The first citrus reference genome (Citrus x clementina) has been publicly available since 2011; however, previous studies in citrus have not utilized the whole genome for LTR-RT marker development. In this study, 3959 full-length LTR...

Identification of molecular processes that differ among Scots pine somatic embryogenic cell lines leading to the development of normal or abnormal cotyledonary embryos

Several coniferous species can today be propagated through somatic embryogenesis, but for species belonging to the Pinus genus, there are still problems related to the small number of genotypes from which embryogenic cultures can be established and the low yield of high-quality cotyledonary embryos. In order to pinpoint molecular processes that might be disturbed during somatic...

Quantitative proteomics of pomegranate varieties with contrasting seed hardness during seed development stages

In pomegranate (Punica granatum), seed hardness is an important trait directly affecting fruit marketability. However, seed formation in pomegranate has not been well studied. We investigated the genetic mechanism underlying pomegranate seed hardness by comparing protein expression profiles between soft- and hard-seeded varieties 60 and 120 days after flowering. We identified...

Walnut: past and future of genetic improvement

Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known. Persian walnuts, native to the mountain valleys of Central Asia, are grown worldwide in temperate areas. World production exceeds three million tons since 2012, mostly provided by China, the USA, and Iran. Despite very ancient culture of walnut...

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). ‘Honeycrisp’ and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards...

Fruit shape and reproductive self and cross compatibility for the performance of fruit set in an andromonoecious species: Xanthoceras sorbifolium Bunge

A replicated 6 × 6 complete diallel mating among six fruit shape types of Xanthoceras sorbifolium (yellowhorn), an andromonoecious plant known for its exceedingly low fruit and seed set, was conducted to investigate the species mating system. This mating design was implemented to investigate the relationship between fruit shape type and fruit yield, finding the most productive...

Genetic variation in resistance of Norway spruce seedlings to damage by the pine weevil Hylobius abietis

Regeneration of northern conifer forests is commonly performed by reforestation with genetically improved materials obtained from long-term breeding programs focused on productivity and timber quality. Sanitary threats can, however, compromise the realization of the expected genetic gain. Including pest resistance traits in the breeding programs may contribute to a sustainable...

Worldwide translocation of teak—origin of landraces and present genetic base

Teak (Tectona grandis Linn. f.) is one of the major plantation timbers of the world. The species is native to India, Myanmar, Thailand and Laos in South East Asia but was translocated to several countries in Africa and Central and South America during the past century. Today, large areas of plantations are grown outside the species native range. It is speculated that genetic...

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or differences in the level of expression of genetic differences among environments. G×E can reduce heritability and overall genetic gain, unless breeding programmes are structured to address different categories...

Gene flow between vicariant tree species: insights into savanna-forest evolutionary relationships

Studying the genetic structure of vicariant species (i.e., closely related species that occupy ecologically distinct yet adjacent habitats) can shed light on the evolution and divergence of species with different ecological requirements. A previous phylogeographic study identified chloroplast DNA haplotype sharing between two vicariant tree species, one from forest (Hymenaea...

QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

Sitka spruce (Picea sitchensis (Bong.) Carr) is the most common commercial plantation species in Britain and a breeding programme based on traditional lines has been in operation since the early 1960s. Rotation lengths of 40-years have led breeders to adopt a process of indirect selection at younger ages based on traits well correlated with final selection, but still the...

Patterns of additive genotype-by-environment interaction in tree height of Norway spruce in southern and central Sweden

Genotype-by-environment (G × E) interaction for tree height measured at ages 7 to 13 was investigated in 20 large open-pollinated progeny trials for Norway spruce (Picea abies (L.) H. Karst.) in southern and central Sweden. Factor analytic method using spatially adjusted data and a reduced animal model was used to explore the pattern of G × E interaction. Extended factor analyses...

Transcriptome analysis provides insights into wood formation during larch tree aging

Tree age affects wood formation and yield. However, the underlying mechanisms are poorly understood, particularly at the molecular level. In this study, we investigated the transcriptomic changes of the uppermost main stems of Larix kaempferi in an entire rotation period using the RNA-Seq method. In total, ∼151 million reads were obtained from the stems of 1-, 2-, 5-, 10-, 25...

Genetic structure of dioecious and trioecious Salix myrsinifolia populations at the border of geographic range

Gene flow in plant populations is heavily affected by species sexual systems. In order to study the effect of sexual systems on genetic structure, we examined plastid and nuclear DNA of 12 dioecious (males and females) and 18 trioecious (males, females and hermaphrodites) populations of Salix myrsinifolia—a boreal shrub with slow range expansion. Populations were located along...

High-throughput sequencing reveals that pale green lethal disorder in apple (Malus) stimulates stress responses and affects senescence

Pale green lethal (PGL) is a recessive genetic disorder of apple (Malus) characterized by severe chlorophyll deficiency and seedling lethality. Following germination, seedlings cannot photosynthesize and die at the cotyledon stage. We previously reported that the genetic and biochemical basis of PGL is due to a loss-of-function mutation in a gene required for the biosynthesis of...

Broad-scale genetic homogeneity in natural populations of common hazel (Corylus avellana) in Ireland

Hazel (Corylus avellana) has been a key species in European woodlands throughout the Holocene (10 KYA–present). Like many tree species, it is increasingly under threat from climate change, habitat loss and fragmentation, invasive species and emergent pathogens. As knowledge of the genetic structure of natural populations of trees is vital for managing these threats, as well as an...

Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in Norway spruce

Adverse genetic correlations between growth traits and solid-wood, as well as fiber traits are a concern in conifer breeding programs. To evaluate the impact of selection for growth and solid-wood properties on fiber dimensions, we investigated the inheritance and efficiency of early selection for different wood-fiber traits and their correlations with stem diameter, wood density...

Mating dynamics of Scots pine in isolation tents

Seed orchards are forest tree production populations for supplying the forest industry with consistent and abundant seed crops of superior genetic quality. However, genetic quality can be severely affected by non-random mating among parents and the occurrence of background pollination. This study analyzed mating structure and background pollination in six large isolation tents...