Tree Genetics & Genomes最新文献

Wisconsin is the world’s leading producer of cranberries (Vaccinium macrocarpon Ait.; 2n = 2x = 24). The state produces over twenty-thousand acres that contribute to more than 50% of the global total production, with more than one billion dollars in value. Cranberry growers in the “central sands” of Wisconsin have been experiencing yield decline due to vegetative unproductive genotypes, popularly known as “Barren Berry’’, which consistently remain vegetative and produce no fruit. The purpose of this study was to compare visual inspection in the field to DNA fingerprinting for the early detection of unproductive/barren genotypes. Additionally, the study served as a survey of unproductive genotypes in central Wisconsin, the largest growing region in the world. A total of 839 cranberry leaf samples, from 14 growers representing plantings to four cultivated varieties, were submitted for DNA testing of two visually determined phenotypes: unproductive or barren (n = 646; those that produced little to no fruit), versus productive or fruiting (n = 193). We conducted genetic fingerprinting on the leaf tissue using nine microsatellite markers previously shown to differentiate cranberry genotypes. This study identified a barren berry genotype unique to central Wisconsin, which we denoted “Barren Berry 1”. This genotype accounted for 43% of samples submitted as the barren berry phenotype. Genetic fingerprinting revealed sixty-five different genotypes in beds which were thought to be monocultures of just four cultivated genotypes. Early detection of genetic contamination through visual inspection, genetic testing, and responsible propagation can drastically aid in the management and longevity of cranberry beds, and in turn save time and money to the growers.

Progeny trials in tree breeding are often laid out using blocked experimental designs, in which families are randomly assigned to plots and several trees are planted per plot. Such designs are optimized for the assessment of family effects. However, tree breeders are primarily interested in assessing breeding values of individual trees. This paper considers the assessment of heritability at both the family and tree levels. We assess heritability based on pairwise comparisons among individual trees. The approach shows that there is considerable heterogeneity in pairwise heritabilities, primarily due to the differences in both genetic as well as error variances among within- and between-family comparisons. Our results further show that efficient blocking positively affects all types of comparison except those among trees within the same plot.

Despite extensive introductions of Eucalyptus germplasm to Brazil in the last 50 years, relatively little is known about the genetic diversity within current breeding programs, particularly for non-mainstream species. A prime example is Eucalyptus benthamii, a subtropical species with a restricted natural range, endangered due to anthropogenic population fragmentation. We used microsatellite markers to reconstruct the pedigrees and estimate diversity within the two most representative pools of E. benthamii germplasm managed in separate, commercial Brazilian breeding populations. The analysis, together with evidence from Australian Tree Seed Centre (ATSC), historical germplasm export data confirmed that the genetic diversity within the two populations is modest. In the two breeding populations, the estimated status number was in the range of 8.5–22.0 per population considering marker-based co-ancestry. Extensive close relatedness and family structure were identified within and across the two populations, confirming that they share a high proportion of founder ancestors. This is likely a result of the narrow genetic base of the initial introductions and subsequent directional selection and breeding. With the increasing importance of E. benthamii in Brazilian plantation forestry, and as further breeding will likely reduce the status number, our study highlights the need for infusions to augment the existing genetic diversity. Complementary to sourcing infusions, implementing breeding strategies that take advantage of the marker-based information reported in this study to carefully manage the pedigree should help to minimise inbreeding. Exchanging unrelated individuals between the two Brazilian breeding populations would also be advantageous.

Knowledge of the genetic diversity and population structure of species can facilitate conservation and guide management programs. However, the type of molecular markers used can affect estimates of genetic divergence and population structure. Here three types of molecular markers were used to estimate the genetic diversity and population structure of Euterpe edulis, a palm endemic to the Atlantic Forest and economically and ecologically important. The objective was to estimate the parameters of genetic diversity and population structure for two other types of molecular markers (SNP and SilicoDArT) in addition to the commonly used one (SSR) to the species. We used single nucleotide polymorphism (SNP), SilicoDArT, and microsatellite (SSR) markers in 138 E. edulis individuals sampled from 15 sites. Euterpe edulis individuals were grouped into 11 clusters using SNPs and SilicoDArT and six groups using SSR data. The SNP and SilicoDArT data showed less divergence between the individuals within each cluster in comparison to the results derived from the SSR data. The probability of reassigning individuals to their cluster of origin revealed an average association with the original clusters was 0.92 for SNPs (n = 100), 0.71 for SSR (n = 8), and 0.99 for SilicoDArT (n = 445). The genetic divergence is high among sites using SNP markers, whereas SSRs showed the largest genetic divergence is found within each site. The overall heterozygosity values for each site in the eight SSR (He = 0.69; Ho = 0.59) markers were almost four times higher than those values inferred using SNPs (data 7833 SNP, He = 0.15; Ho = 0.13; data 100 SNP, He = 0.14; Ho = 0.12). Within each site, we found low inbreeding rates using both markers (SNP and SSR). In addition, population structure analysis identified two strongly supported geographical groups, one northern and one southern Brazilian Atlantic Forest group, for both markers. This study contributes to the understanding of the population genetics and population structure of E. edulis and may have important implications for its conservation. In addition, our results suggest that SNP and SilicoDArT markers are more effective for evaluating population structure, but SSR is more capable of detecting diversity among individuals for this species.

Climate change is having an impact on locally adapted species, including the cork oak (Quercus suber L.), a key tree species in the Mediterranean region especially due to its role in carbon sequestration. Notably, the Maâmora forest in Morocco stands as the largest forest in the Mediterranean basin with the highest diversity compared to similar forests across Morocco. In this study, we genotyped 240 samples from natural populations of cork oak in the Maâmora forest using seven microsatellite markers, to investigate signatures of local adaptation. Using a genomic scan approach, we identified outliers loci experiencing divergent natural selection pressures, which were later correlated with climatic, edaphic, and geographic conditions of the Maâmora forest. Statistical analysis of the data shows a high allelic variation. The detection of outliers, carried out using BayeScan v2.1 software, revealed the presence of two significant outliers loci ZAG20-171 (qvalue = 0.0004) and MSQ4-211 (qvalue = 0.04). The result of the environmental association analysis revealed a significant correlation between locus ZAG20-171 with mean diurnal range, isothermality, annual precipitation, precipitation of the driest month, precipitation of the wettest quarter and altitude. This work aims to help understanding the genetic basis of adaptation in Q. suber L., and thus the selection of suitable provenances for further breeding efforts.

Eastern black walnut, Juglans nigra L., is an economically important tree species valued for its high-quality timber and edible nuts. A regional industry for the species’ nut and kernel products resides in Missouri, where over 9 million kg of hulled in-shell nuts are purchased in masting years. The crop is primarily based upon nuts harvested from wild trees, placing a ceiling on nut volume and quality (e.g. small nut size, dark pellicle color, and 10–14% kernel by weight). Orchards of named cultivars, like ‘Kwik Krop’ and ‘Sparrow’, supply up to 22,000 kg of nuts with a higher kernel percentage (> 26%) and improved quality. Such cultivars often represent chance wild or on-farm seedlings, clonally propagated since the late 1800’s by enthusiasts. Today, continued improvement of eastern black walnut as an orchard crop is limited by a long generation time, delayed expression of important traits, and space requirements – creating a strong need for marker-trait association studies that inform progeny selection. The first linkage map for J. nigra was recently created using the ‘Sparrow’ × ‘Schessler’ F₁ population and loci for phenology traits discovered. The objective of this study is to utilize these genetic resources to detect quantitative trait loci (QTL) and report associated DNA markers for the spur-bearing habit, which promotes precocity and high yield. Using single-year data from the 11-year-old population, we observe that segregation for the spur-bearing habit appears to be recessive and multigenic. Three QTLs (p > 0.99) were identified on linkage group (LG) 8, LG11, and LG16 that explain 7.2%, 8.7%, and 10% of trait variation, respectively. Regions between flanking DNA markers were 3.16 cM, 4.32 cM, and 9.69 cM, respectively. This study is the first to examine the genetic control of bearing habit and yield in eastern black walnut and informs breeders’ approach for their future genetic improvement.

The cultivated apple (Malus domestica Borkh.) is an economically important fruit crop in countries worldwide, including Bosnia and Herzegovina (BIH).The gene bank activities in BIH were initiated in the 1930s and continued until the war in the 1990s, when much of the documentation was lost. Since then, uncoordinated efforts were made to establish apple collections in different regions, but a comprehensive analysis of genetic resources was lacking. This prompted the current study where we present the first thorough overview of the national genetic resources of BIH apples. Thus, we analyzed 165 accessions in the apple gene bank at the Institute for Genetic Resources (IGR) established at Banja Luka using the 20 K apple Infinium^® single nucleotide polymorphism (SNP) array. We combined the results with previously published data on the germplasm collections at Srebrenik and Goražde, genotyped using the Axiom^® Apple 480 K SNP array. In total, 234 accessions were included in the study of which 220 were presumed to be local cultivars and 14 were known international reference cultivars. We identified numerous genotypic duplicates within and between collections and suggested preferred names to be used in the future. We found the BIH germplasm to have relatively few parent-offspring relationships, particularly among local cultivars, which might reflect the country’s history and patterns of apple cultivar introduction. A number of cultivars unique to BIH and a weakly defined genetic group were identified via STRUCTURE analysis, representing interesting targets for future research and preservation efforts.

Given the ease of propagating fruit tree species through cloning, the economic viability of their breeding programs hinges on protecting breeders' rights. This necessitates the development of highly accurate DNA markers for cultivar identification. Here, we present a methodology for the rapid design of cleaved amplified polymorphic sequence (CAPS) markers to discriminate newly bred Japanese citrus cultivars from genetically related cultivars. We first compared the performance of ddRAD-seq and MIG-seq in citrus germplasm. The ddRAD-seq libraries generated using EcoRI and HindIII restriction enzymes yielded the highest number of polymorphisms. Subsequently, ddRAD-seq with EcoRI and HindIII was employed to analyze 29 citrus cultivars and thus identify 331,801 genome-wide polymorphisms. A semi-automated bioinformatics pipeline was then utilized to identify candidate CAPS markers, resulting in the discovery of 14,072 potential markers. Of these candidates, 52 were chosen for validation based on their recognition by the PstI restriction enzyme. This evaluation resulted in the development of 11 highly discriminative CAPS markers. Remarkably, a combination of only six such markers was sufficient to differentiate newly bred cultivars from their genetically related parents. The single restriction enzyme employed for these markers facilitates straightforward multiplexing. Finally, a combination of one multiplex marker testing two loci and four singleplex markers was successfully selected that completely discriminated the cultivars other than the bud sports used in this study. The pipeline established here extends beyond citrus and has the potential to simplify marker development and cultivar protection in various plant species.

Aotearoa New Zealand’s swamp forests have experienced significant habitat loss in fewer than two hundred years. Many of the country’s tree species are endemic with sparse to no genetic information available to underpin conservation strategies. Syzygium maire, Aotearoa’s only endemic Syzygium species, is a culturally and ecologically important component of swamp forest habitats. Unfortunately, populations of S. maire have been greatly reduced, heavily fragmented and are susceptible to the emergent pathogen Austropuccinia psidii (myrtle rust), posing eminent danger of a further decline of the species. We sought to develop genomic resources to inform conservation management of S. maire. To this end, we used long read, high accuracy sequencing technology to produce a highly complete reference quality genome for S. maire. The genome sequence was named ‘Ngā Hua o te Ia Whenua’ by the local Māori tribe where the tree used for genome sequencing grows. We assess whether genome-level divergence with other Myrtaceae may have followed geographic isolation of the species. We detect conservation of large scale synteny between three Syzygium species and Eucalyptus grandis, providing support for the stability of Syzygium genomes across evolutionary time. We annotate genes implicated in fungal pathogen defence, identifying several hundred putative NLR genes, including putative homologs of previously identified Austropuccinia psidii resistance genes. Finally, we evaluate the genetic relationships of individuals of a small, isolated population of trees. We find evidence of high levels of kinship and inbreeding within small and isolated S. maire populations, informing local-scale conservation strategies for the species. Our findings enable practical conservation actions and provide resources for larger scale studies of S. maire and other Syzygium species in the future.

Giam Malut Hopea ferrea Laness (Dipterocarpaceae) is a woody species that has become endangered due to its habitat destruction and overexploitation. In an effort to support and provide conservation and management of this species, we utilized eight microsatellite loci to investigate the genetic diversity and structure of 234 adult trees across eight populations, encompassing its geographic distribution in Vietnam. The genetic diversity of H. ferrea was found to be low in comparison to other dipterocarps, suggesting a reduction in the number of alleles due to anthropogenic activities. Heterozygosity deficits were identified across all studied populations. Interestingly, the coastal populations exhibited higher genetic diversity compared to the Highlands and southeast populations. Bottleneck effects were detected in the majority of populations, with the exception of the two Highlands populations of Chu Mon Ray and York Don. These effects indicated a reduction in the population sizes. The results of genetic differentiation mirrored the genetic structure and revealed three major clusters corresponding to the three distribution areas of the species. A low level of genetic differentiation among populations (F_ST=0.146) was detected, consistent with the AMOVA analysis. Geographic distance and anthropogenic activities emerged as the major factors limiting gene exchange among populations. Based on these findings, we propose conservation measures for this endangered species.