Genetic mapping of a locus controlling the intergeneric hybridization barrier between apple and pear Abstract Hybridizations involving different species are often hindered because of incompatibility reactions. Although these reproductive barriers have been observed in many plant species, the underlying mechanisms remain to be comprehensively elucidated. In this study, we detected a hybridization barrier between apple (Malus × domestica) and pear (Pyrus spp.) belonging to different genera in the subtribe Malinae of the family Rosaceae. Pollination experiments revealed that Pyrus pyrifolia (Japanese pear) pollen is compatible with Malus pistils, whereas Pyrus communis (European pear) pollen is not. These results imply there is a distinct cross-(in)compatibility reaction occurring in Pyrus species. Based on the varying pollen tube behaviors among Pyrus species, genetic analysis was conducted to identify the genomic region responsible for the intergeneric barrier. Malus–Pyrus intergeneric hybrids were used to detect distorted segregation regions by combining genome sequencing and fine-scale genotyping data. We defined a single locus on chromosome 5, in which P. pyrifolia-derived alleles were exclusively inherited to the intergeneric hybrids from the Pyrus interspecific hybrid. Of the 235 genes in this genomic region, 80 exhibited a specific pollen-expression pattern, including genes involved in self-incompatibility reactions. These candidate genes are herein discussed regarding their possible functions related to reproductive isolation.

Crown morphology in Norway spruce ( Picea abies [K arst .] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm Abstract Trees growing at high altitude or latitude have to be adapted, among others, to the lower temperatures, a shorter vegetation period, heavier snow load, and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day–night shift and seasonal change. Potentially adaptive “candidate” genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation and phenotypic traits measured in natural populations, and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterized by superior resistance to snow breakage in regions with heavy snowfall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony), and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait-related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.

Genetic diversity of oolong tea ( Camellia sinensis ) germplasms based on the nanofluidic array of single-nucleotide polymorphism (SNP) markers Abstract As one of the most popular Chinese tea products, oolong tea involves the most complicated manufacturing process and the most abundant tea germplasm resources. However, the unclear genetic backgrounds of oolong tea germplasms have been biological limitations for tea breeding and quality control. In this study, high-throughput SNP technology was used to analyze the genetic diversity of 100 oolong tea landraces and cultivars. Ninety-six pairs of primers were selected and validated from the expressed sequence tag (EST) database of Camellia sinensis. The results verified 75 SNP loci that are able to accurately and efficiently determine the genetic relationships among Chinese oolong tea germplasms. The DNA fingerprints of 4 main oolong tea-producing areas were constructed by tracing the information of each site of the SNP. The Guangdong oolong tea germplasms were a relatively distinct group, while the genotypes of Taiwan oolong tea were similar to those of populations in Fujian. The tea germplasms in Southern and Northern Fujian had the largest intersections, and they also showed their own characteristics. Our results provide guidance for the identification, integration, and selection of parents for tea plant germplasms. Moreover, our study provides an effective tool to protect the diversity of tea germplasms and to assist in future breeding work.

Phylogeography and population dynamics of an endemic oak ( Quercus fabri Hance) in subtropical China revealed by molecular data and ecological niche modeling Abstract High numbers of endemic plants exist in subtropical China, but there have been few investigations of the phylogeography and dynamic history for endemic tree species in this region. In this study, we explored the phylogeographic pattern of Quercus fabri, an endemic oak species in subtropical China, to assess the effects of past geographical and climatic changes on the evolutionary history of this deciduous species using three chloroplast DNA (cpDNA) fragments and the internal transcribed spacer region (ITS) and ecological niche modeling (ENM). The cpDNA fragments differentiated three phylogeographical groups among Q. fabri populations. A BEAST-derived chronogram based on the cpDNA haplotypes indicated that the initial divergence of Q. fabri probably occurred during the late Miocene (12.33 Ma), whereas haplotype divergence time could date back to the late Pliocene to early Pleistocene. ENM showed that the suitable areas contracted during the last glacial maximum (LGM) and expanded in the warm period during the Pleistocene. Consistently, both the cpDNA and ITS datasets suggested that population expansion occurred after the LGM period (ca. 13–14 kyr) for Q. fabri. Demographical analyses based on multiple genetic datasets and a coalescent-based method also suggested a shrinkage–expansion trend for the effective population sizes of Q. fabri during the glacial–interglacial periods in the Quaternary. Our results suggest that the Neogene and Pleistocene were important periods for triggering species differentiation and intraspecific diversification in Q. fabri, thereby providing insights into the effects of environmental changes in the Quaternary on the population dynamics of endemic tree species in subtropical China.

Widely distributed variation in tolerance to Phytophthora palmivora in four genetic groups of cacao Abstract The tropical tree Theobroma cacao is the source of chocolate, and its seeds are a major export from many producing countries in Central and South America, Africa, and Asia. Every year, 30–40% of pre-harvest yield is lost due to disease damage. Host plant resistance is the most efficient and environmentally friendly approach for disease management. Historically, cacao germplasm resources have been underutilized in efforts to introduce novel sources of disease tolerance into breeding programs. Maintenance of cacao germplasm also relies on clonally propagated live collections, as cacao seeds do not exhibit dormancy and cannot be stored for more than a few weeks. In this study, we use a 90 SNP array to verify genetic identity of a set of clones in the International Cocoa Collection at CATIE, Costa Rica, and assign the clones into known genetic groups. We also used a detached leaf inoculation technique to measure the susceptibility of 60 genotypes to Phytophthora palmivora, a major cacao pathogen with global importance. We identified 24 genotypes with disease tolerance statistically similar to a standard tolerant variety (SCA6) and another 24 which performed similarly to a standard susceptible variety (ICS1). Our results indicate that each of the four included genetic groups show variability for quantitative resistance to P. palmivora. These results provide a foundation for future genomic and transcriptomic analysis of disease tolerance and susceptibility in the field at CATIE and provide guidelines for breeders searching for novel sources of tolerance that can be introduced into breeding programs.

Hierarchical genetic and spatial structure among varieties and populations of Hymenaea stigonocarpa (Fabaceae) in Brazilian savannah Abstract Approaches in population genetics decompose species genetic variation at hierarchical level, understanding the action of microevolutionary processes at spatial scales. We evaluated the taxonomically complex species Hymenaea stigonocarpa, a tree species distributed in central Brazil, presenting three botanical varieties weakly distinguished by morphological traits. We aimed to investigate the spatial genetic structure of populations of H. stigonocarpa along Cerrado biome, assessing genetic differentiation and the existence of hybridization zones in this species. We genotyped 901 plants from 28 local populations using nine nuclear microsatellite loci. Analyses of genetic diversity, Bayesian inference estimated genetic differentiation and migration rate among populations and varieties. Mantel tests and sPCA evaluated spatial pattern of genetic variation. We observed that H. stigonocarpa var. brevipetiolata presented larger genetic differentiation compared to H. stigonocarpa var. stigonocarpa and H. stigonocarpa var. pubescens (FCT = 0.175). Bayesian approaches supported a genetic different cluster and hybridization process in sympatric populations for H. stigonocarpa var. brevipetiolata. Migration rate was high and not significantly higher among varieties, confirming the existence of hybridization. Spatial correlations were relatively low, but with exponential decrease of genetic similarity along of the geographic space. Spatial genetic structure was higher for H. stigonocarpa var. brevipetiolata and local structures were found with sPCA, indicating that neighboring populations are genetically different mainly in populations of eastern Cerrado. The genetic clusters are not congruent with the vegetative characters used to recognize the three botanical varieties, which should be viewed with skepticism. Our genetic analyses strongly support the need for a taxonomic review.

Correction to: Genome-wide association studies of bark texture in Populus trichocarpa The co-author Jin Zhang was unintentionally forgotten on the original author list. The correct Author list is presented in this paper.

Genetic characterization of fragmented populations of Cinchona officinalis L. (Rubiaceae), a threatened tree of the northern Andean cloud forests Abstract Cinchona officinalis L., a tree species endemic to the cloud forests of the northern Tropical Andes, has suffered from historical bark harvesting for extraction of antimalarial compounds and has also experienced recent demographic losses from high rates of deforestation. Most remnant populations are found in severely degraded habitat on the edges of pastures while a minority are protected in private reserves. The goals of our research were to assess the genetic diversities of fragmented populations of C. officinalis in the Loja province of southern Ecuador, characterize their phylogeographic distribution with respect to the region’s complex topography, and identify priority populations for conservation. Five nuclear microsatellite loci and the chloroplast rps16 intron were used to analyze six populations. Moderate levels of genetic diversity were found in all populations although the more remote southern population (Angashcola) had slightly higher heterozygosity and allelic richness. There were no indications of recent genetic bottlenecks although an rps16 intron haplotype was fixed in four populations. Genetic distance analysis based on microsatellite data placed the four easternmost populations in the same clade while the Angashcola population was the most divergent. Also, the most frequent rps16 intron haplotype in Angashcola was not found in any other population. Although each of the studied populations should be protected from further deforestation and agricultural expansion, the Angashcola population deserves highest conservation priority.

Clinal variation in growth cessation and FTL2 expression in Siberian spruce Abstract Forest trees exhibit strong patterns of local adaptation in phenological traits along latitudinal gradients. Previous studies in spruce have shown that variation at genes from the photoperiodic pathway and the circadian clock are associated to these clines but it has been difficult to find solid evidence of selection for some of these genes. Here, we used growth cessation, gene expression, and single nucleotide polymorphism (SNP) data at two major candidate loci, FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (FTL2) and GIGANTEA (GI), as well as at background loci from a latitudinal gradient in Siberian spruce (Picea obovata) populations along the Ob River to test for clinal variation in growth cessation and at the two candidate genes. As in previous studies, there was a strong latitudinal cline in growth cessation that was accompanied by a significant cline in the expression of FTL2. Expression of FTL2 was significantly associated with allele frequencies at some of the GI’s SNPs. However, the cline in allele frequency at candidate genes was not as steep as in a Norway spruce cline and in a parallel Siberian spruce cline studied previously and nonsignificant when a correction for population structure was applied. A McDonald-Kreitman test did not detect decisive evidence of selection on GI (p value = 0.07) and could not be applied to FTL2 because of limited polymorphism. Nonetheless, polymorphisms contributed more to the increased neutrality index of PoGI than to that of control loci. Finally, comparing the results of two previously published studies to our new dataset led to the identification of strong candidate SNPs for local adaptation in FTL2 promoter and GI.

The origin and genetic variability of vegetatively propagated clones identified from old planted trees and plantations of Thujopsis dolabrata var. hondae in Ishikawa Prefecture, Japan Abstract Clonal plantations of Thujopsis dolabrata var. hondae have been established in Ishikawa Prefecture, Japan, since at least the 1800s. Historical planting of the species has led to the development of vegetatively propagated local cultivars, which originated from ‘donor’ trees that have often been conserved in sacred groves or avenues at shrines and temples. These donor trees must have been selected from natural populations. In this study, we estimated the origin and genetic variability of clones identified among old planted trees and clonal plantations of T. dolabrata var. hondae, using 19 microsatellite markers. We discovered 12 clones among old planted trees, including 5 identical to members of a set of 14 we previously identified in plantations (giving 21 clones in total). Based on analyses combining assignment and exclusion tests, we inferred origins of 8 of those 21 clones: 6 may have originated from a natural population distributed in Ishikawa, 1 from Hokkaido and Aomori, and the other from Iwate and Yamagata, suggesting the clones constituting cultivars have multiple origins. The clones identified in plantations have significantly lower genetic variability and higher relatedness, indicating that clones of cultivars have a much narrower genetic base than those of natural populations. We suggest new clones selected from natural populations elsewhere, as well as Ishikawa, are needed for future breeding of T. dolabrata var. hondae to develop clonal forestry for this species.