Tree Genetics & Genomes最新文献

Abstract

The MYB family is one of the largest families of transcription factors, in which the R2R3-MYB subgroup plays a crucial role in various biological processes. R2R3-MYBs in Populus davidiana × Populus bolleana have, however, not been systematically investigated. Here, based on the gene annotation of P. davidiana × P. bolleana genome sequence, all PdbR2R3-MYB transcripts were identified. These PdbR2R3-MYBs were classified into 29 subgroups (C2 to C30) according to the phylogenetic analysis of Arabidopsis thaliana AtR2R3-MYBs. The analysis of gene structures and protein motifs showed the conservation and evolution of PdbR2R3-MYBs. The cis-acting elements in the promoters of PdbR2R3-MYB genes were predicted, and the results indicated an abundance of abscisic acid and defense- and stress-responsive elements. The results of qRT-PCR revealed that nine PdbR2R3-MYB genes were differentially expressed in various tissues and can be regulated by drought stress; thus, these genes may play key roles in the response of plants to drought stress. In addition, the expression of PdbMYB5 and PdbMYB102 was significantly higher than those of the other seven MYB genes; hence, PdbMYB5 and PdbMYB102 overexpressing (OE) and silenced (SE) poplar plants were generated to investigate drought stress tolerance. The PdbMYB5 and PdbMYB102 OE plants showed enhanced reactive oxygen species scavenging capability, less cell damage, and high expression levels of the SOD and POD genes, whereas the SE plants showed the opposite results, thus suggesting that PdbMYB5 and PdbMYB102 conferred enhanced drought tolerance to the plants. This study provided insights into gene characterization, structure, evolution, expression, and function of the PdbR2R3-MYB family in poplar plants.

Abstract

Schima superba (Theaceae) is widely distributed in subtropical China, and is the main timber and ecological afforestation tree species. This study aimed to provide a practical basis for the genetic improvement of wood traits of Schima superba. Herein, 10-year-old, half-sib families S. superba trees were used to reveal the genetic variation and control of growth traits and wood traits, as well as the correlation between them. The results revealed significant differences in tree height, DBH, and wood basic density among families. Furthermore, the differences in wood anatomical traits between families increased with age. The order of phenotype and genetic variation among families from large to small was DBH, tree height, vessel, fiber, and wood basic density. The phenotype variation and genetic variation of wood anatomical traits also increased with age. Heritability estimates revealed that wood basic density, DBH, and tree height were under stronger genetic control; fiber and vessel were under moderate genetic control. The correlation results showed that tree height, DBH, and wood basic density could be selected independently. Wood basic density and wood anatomical traits together could be improved. Moreover, based on the selection traits of DBH and WBD, families with excellent growth and wood traits were selected using breeding values.

Abstract

DNA methylation is an important epigenetic mark that plays a crucial role in regulating various biological processes and adaptation to environmental conditions in both plants and animals. At present, there are no reports on the systematic analysis of the DNA-(cytosine-5) methyltransferase (C5-MTase) and demethylase (dMTase) gene families from the cacao (Theobroma cacao) genome. In this study, a comprehensive bioinformatic analysis identified the presence of seven C5-MTases (TcC5-MTases) and three dMTases (TcdMTases) in cacao. According to the sequence similarity, and conserved motif and domain architecture, TcC5-MTases were phylogenetically classified into METHYLTRANSFERASE 1 (TcMET1), CHROMOMETHYLASE (TcCMT1-3), DOMAINS REARRANGED METHYLASE (TcDRM1/2, TcDRM3), and de novo DNA METHYLTRANSFERASE 2 (TcDNMT2), and TcdMTases were classified into DEMETER (TcDME), REPRESSOR OF SILENCING 1 (TcROS1, also known as DEMETER-LIKE 1 (TcDML1)), and TcDML3 subfamilies. These genes were distributed randomly on six chromosomes. Moreover, most of the TcC5-MTases and TcdMTases were putatively localized in the nucleus, except TcDRM1/2 and TcDRM3, which were found in chloroplasts. Further analysis of cis-acting regulatory elements (CREs) in the promoter regions TcC5-MTase and TcdMTase genes inferred the presence of multiple CREs, especially stress-responsive, light-responsive, and hormone-responsive elements. Additionally, the analysis of protein–protein interaction networks revealed interactions among TcC5-MTases and with other proteins in T. cacao, such as S-adenosyl-L-homocysteine hydrolase and histone deacetylases, suggesting potential crosstalk among DNA methylation, the methionine cycle, and histone deacetylation. These interactions provide valuable insights into the complexity of regulating plant methylation levels. Collectively, the findings of this study provide a framework for further functional characterization of these genes and unravel the epigenetic mechanisms underlying growth and development, as well as adaptations to stress conditions in cacao.

Abstract

In tree species, inbreeding due to selfing or biparental mating may decrease offspring adaptation and growth due to inbreeding depression (ID). Degenerative effects of ID, mainly reduction in productivity and survival, are undesirable for ex-situ conservation, improvement, and environmental and commercial reforestation of tree species. The effects of ID resulting from self-fertilization and biparental inbreeding were assessed for the traits cylindrical volume and survival in juvenile individuals of Hymenaea stigonocarpa in a progeny test (0.83 ha) at 4 and 7 years of age. The progeny test was established for ex situ conservation in the state of Mato Grosso, Brazil, and was based on seeds collected from a wild population. Nine microsatellite loci were used to genotype 48 adult (plot = 4.3 ha) and 612 juvenile samples to determine spatial genetic structure (for adults), inbreeding, mating system, and pollen dispersal pattern. Spatial genetic structure was observed up to 82 m. Reproduction occurred mainly by outcrossing, with low rates of selfing (7.5%) and biparental inbreeding (13.2%). Mating was not random due to the fat-tail pollen dispersal pattern, resulting in high pollen immigration (70.1%) and low mean pollen dispersal distance (105 m) within the sample area. Inbreeding was observed only in juveniles, indicating selection against inbred individuals between juvenile and adult stages. The volume trait showed higher ID for biparental inbreeding (41.5–44.0%) than for self-fertilization (29.1–42.6%). Volume also showed greater ID than survival. Our results show that even low rates of selfing and biparental inbreeding can decrease the productivity of H. stigonocarpa plantations.

Cork oak (Quercus suber L.) is an essential species of the Mediterranean region. In Morocco, it represents a source of life and is a noble species for many populations. The Maâmora forest, situated in Morocco, is recognized as the largest forest in the Mediterranean basin and displays the highest diversity compared to other forests in its distribution area. This study aimed to establish a genetic database of 240 individuals from Maâmora forest using seven SSR markers. Through a series of statistical analyses, we determined the level of diversity and genetic structure and created a core collection. Statistical analysis of the data showed a high degree of allelic variation, generating 47 alleles with an average of 6.71 alleles per locus. Furthermore, a high percentage of polymorphisms and a high Shannon index were observed. Intra-population genetic diversity was found to be high (86%) compared to inter-population diversity (14%). A low level of genetic differentiation (Gst = 0.12) and high gene flow were identified, consistent with the results obtained from the analysis of molecular variance (AMOVA). This suggests a possible capacity for the species to adapt to environmental conditions. A core collection of 18 genotypes was constructed, which included all the private alleles that were detected in this study. This core collection exhibited similar and crucial diversity to that identified in the initial collection, as verified by a series of genetic diversity and structural analyses. This research advocates populations and individuals for further studies on adaptation in order to improve and conserve this valuable resource in the future.

Abstract

The genes ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) encode the biosynthesis of alkane waxes, a key component of the plant cuticle. To study the evolution of CER1 and CER3 in a highly diverse group of eucalypts, we performed a genome-wide survey using recently released genome assemblies of 28 Myrtaceae species, with 22 species from the main eucalypt lineage and 6 non-eucalypt Myrtaceae tree species. We manually annotated 250 genes and pseudogenes, identifying a near-ubiquitous single copy of CER3 and 2 to 10 CER1 gene copies per Myrtaceae species. Phylogenetic analysis suggested that copy number variation in eucalypts is due to multiple tandem duplication events, both ancient (shared by all Myrtaceae species studied) and relatively recent (present only in eucalypts). Inter-chromosomal translocations were discovered for both CER1 and CER3, along with recurrent loss of often the same CER1 introns in the WAX2 domain, the domain that is essential for wax production. Despite the varied environments occupied by the eucalypt species in this study, we did not find statistically significant associations between intra-genic structural changes or CER1 copy number and aspects of the environment they occupy (including aridity). The challenge is now to explain the species-specific evolutionary histories that contributed to the observed variation in CER1 and the extent to which it may contribute to the adaptability of eucalypts.

Genotype-environment interaction is pervasive in forest genetics. Delineation of spatial breeding zones (BZs) is fundamental for accommodating genotype-environment interaction. Here we developed a BZ classification pipeline for the forest tree Eucalyptus globulus in 2 Australian regions based on phenotypic, genomic, and pedigree data, as well on a detailed environmental characterization (“envirotyping”) and spatial mapping of BZs. First, the factor analytic method was used to model additive genetic variance and site–site genetic correlations (r_B) in stem volume across 48 trials of 126,467 full-sib progeny from 2 separate breeding programs. Thirty-three trials were envirotyped using 145 environmental variables (EVs), involving soil and landscape (71), climate (73), and management (1) EVs. Next, sparse partial least squares-discriminant analysis was used to identify EVs that were required to predict classification of sites into 5 non-exclusive BZ classes based on r_B. Finally, these BZs were spatially mapped across the West Australian and “Green Triangle” commercial estates by enviromic prediction using EVs for 80 locations and 15 sets of observed climate data to represent temporal variation. The factor analytic model explained 85.9% of estimated additive variance. Our environmental classification system produced within-zone mean r_B between 0.76 and 0.84, which improves upon the existing values of 0.62 for Western Australia and 0.67 for Green Triangle as regional BZs. The delineation of 5 BZ classes provides a powerful framework for increasing genetic gain by matching genotypes to current and predicted future environments.

During the process of almond (Prunus dulcis) domestication, essential traits, which gave plants the plasticity for facing unstable environmental conditions, were lost. In general, the domestication process often narrows the natural genetic diversity. Modern selections (i.e., breeding programs) dramatically accelerated this genetic bottleneck trend to a few successful almond cultivars, which are presently the founders of most commercial cultivars worldwide. The concept of utilizing wild species as a source for important traits and for the enrichment of the gene pool was deeply discussed in previous studies. However, in almonds and other Prunus species, deliberate utilization of wild species as a genetic resource for breeding programs is quite rare. To address these significant challenges, we generated an interspecific F1 population between the Israeli almond cultivar Um el Fahem (UEF) and a specimen of a local wild almond species, Prunus arabica (P. arabica), originating from the Judea desert. This interspecific F1 population possesses high phenotypic variability, and sixteen segregating traits were phenotyped. Among the segregating traits, we were able to genetically associate six agriculturally important traits, such as leaf chlorophyll content (LCC), flower size, and fruit size. The alleles for Self-Compatibility (SC) and kernel bitterness were previously mapped in almond and were reexamined on the background of the distinctive wild genetic material of P. arabica. Finally, phenotypic interactions between traits were suggested, such as rootstock perimeter and canopy area that were positively correlated with total yield in the F1 population. This study is a first step towards developing a well-characterized almond interspecies genetic population. The availability of such a genetic tool with detailed phenotypic analysis is crucial to address and explore the profound influence of almond wild species in Prunus genetic research and breeding. By using the interspecific population as the infrastructure, we show the advantages and importance of utilizing wild relatives.

Supplementary information: The online version contains supplementary material available at 10.1007/s11295-024-01668-4.

Tropical rainforests host exceptional biodiversity and provide important ecosystem services, but they are facing anthropogenic and climatic threats. Preserving the genetic diversity of forest tree populations is essential for their capacity to adapt and exhibit resilience to environmental changes and anthropogenic pressures. Here, we collected conservation genetic baseline information for the heavily exploited timber tree Dicorynia guianensis Amshoff (Fabaceae) at the regional and local levels in French Guiana. Based on genotyping at five microsatellite loci in 1566 individuals collected in 23 forest locations, we documented the genetic differentiation of locations from the West of French Guiana and identified distinctive genetic diversity patterns with higher genetic diversity and some bottlenecked sites in the East and inland. The regional population genetic structure is likely the result of past population isolation in distinct Pleistocene refuges and different demographic histories potentially influenced by Holocene drought periods or palaeofires. Assessment of spatial genetic structure (Sp from 0 to 0.028) in five intensively sampled locations yielded estimates of Wright’s neighborhood size of 35 to 313, indicative of restricted dispersal and local metapopulation dynamics, and useful as baseline information to assess the effects of selective logging for conservation management. These results support the current management strategies with low impact extraction of D. guianensis in three zones of the French Guiana permanent forest domain and allow us to make recommendations for further research and management to best preserve its genetic diversity and adaptive potential.

The conservation of genetic diversity is a crucial aspect of forest tree breeding programs, necessitating strategies for its safeguard. Here, the extent of genetic diversity was assessed in 260 Chinese pine (Pinus tabuliformis Carr.) germplasm samples from five provenances using 24 SSR markers. We systematically compared various methods for constructing a core collection aimed at conserving genetic diversity and the results revealed substantial genetic diversity within this germplasm collection. Extensive gene exchange was observed among four of the sampled five provenances which resulted in forming two genetically distinctive groups. To construct the core collection, six different sampling strategies (PowerCore, Power marker_allele number, Power marker_gene entropy, Power marker_gene diversity, Corehunter, and genetic distance-based) and five different sampling sizes (ranging from 10 to 30%) were employed. Comparative analysis of genetic diversity parameters was conducted across the identified 26 subsets, utilizing the PowerCore strategy as the primary approach for capturing all allelic variation present in the core collection, which consisted of only 61 individuals. A supplementary collection of 20 individuals with high genetic variation was identified to provide a final core collection of 81 individuals, representing 31.2% of the initial collection. The constructed core collection effectively captured the genetic diversity present in the initial collection and serves as a valuable resource for preserving genetic richness within the breeding population.