Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies

Genetic Variation Analysis and Development of KASP Marker for Leaf Area and Hight in Southern-Type Populus deltoides

Populus deltoides holds significant ecological and economic importance and is a crucial gene donor for the world's staple poplar varieties. To select and breed P. deltoides with improved agronomic traits, nine growth and leaf traits were examined in 375 different genotypes, assessing their genetic diversity and performing correlation and comprehensive ranking analyses. Phenotyping results were then utilized to screen a total of 2,009,263 SNP (single nucleotide polymorphism) loci significantly associated with the nine phenotypic traits. A total of 45 SNP loci exhibited significant associations with growth traits based on a general linear model (GLM) analysis. By analyzing the Linkage disequilibrium (LD) block of five SNP loci with significant leaf area and height, we identified five candidate genes related to leaf area and height. Three of the five SNP loci were successfully validated using KASP (kompetitive allele-specific PCR) assays. One loci Chr08_16007979 was closely linked with leaf area, and two loci Chr05_12148738, and Chr05_17106547 were closely linked with height. The developed functional KASP markers offer valuable insights for subsequent further marker-assisted breeding and genetic improvement studies in southern-type poplars.

Applications of CRISPR Technologies in Forestry and Molecular Wood Biotechnology

Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests. This review provides a comprehensive overview of CRISPR applications in forestry, exploring its potential for enhancing disease resistance, improving abiotic stress tolerance, modifying wood properties, and accelerating growth. We discuss the mechanisms and applications of various CRISPR systems, including base editing, prime editing, and multiplexing strategies. Additionally, we highlight recent advances in overcoming key challenges such as reagent delivery and plant regeneration, which are crucial for successful implementation of CRISPR in trees. We also delve into the potential and ethical considerations of using CRISPR gene drive for population-level genetic alterations, as well as the importance of genetic containment strategies for mitigating risks. This review emphasizes the need for continued research, technological advancements, extensive long-term field trials, public engagement, and responsible innovation to fully harness the power of CRISPR for shaping a sustainable future for forests.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

High-yield hybrid breeding of Camellia oleifolia based on ISSR molecular markers

BACKGROUND

C. Oleifera is among the world's largest four woody plants known for their edible oil production, yet the contribution rate of improved varieties is less than 20%. The species traditional breeding is lengthy cycle (20-30 years), occupation of land resources, high labor cost, and low accuracy and efficiency, which can be enhanced by molecular marker-assisted selection. However, the lack of high-quality molecular markers hinders the species genetic analysis and molecular breeding.

RESULTS

Through quantitative traits characterization, genetic diversity assessment, and association studies, we generated a selection population with wide genetic diversity, and identified five excellent high-yield parental combinations associated with four reliable high-yield ISSR markers. Early selection criteria were determined based on kernel fresh weight and cultivated 1-year seedling height, aided by the identification of these 4 ISSR markers. Specific assignment of selected individuals as paternal and maternal parents was made to capitalize on their unique attributes.

CONCLUSIONS

Our results indicated that molecular markers-assisted breeding can effectively shorten, enhance selection accuracy and efficiency and facilitate the development of a new breeding system for C. oleifera.

A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network

Metabolism results from enzymatic- and non-enzymatic interactions of several molecules, is easily parameterized with the dissociation constant and occurs via biochemical networks. The dissociation constant is an empirically determined parameter and cannot be used directly to investigate in silico models of biochemical networks. Here, we develop and present an algorithm to define, compute and assess the relevance of the probable dissociation constant for every reaction of a biochemical network. The reactants and reactions of this network are modelled by a stoichiometry number matrix. The algorithm computes the null space and then serially generates subspaces by combinatorially summing the spanning vectors that are non-trivial and unique. This is done until the terms of each row either monotonically diverge or form an alternating sequence whose terms can be partitioned into subsets with almost the same number of oppositely signed terms. For a selected null space-generated subspace the algorithm utilizes several statistical and mathematical descriptors to select and bin terms from each row into distinct outcome-specific subsets. The terms of each subset are summed, mapped to the real-valued open interval [Formula: see text] and used to populate a reaction-specific outcome vector. The p1-norm for this vector is then the probable dissociation constant for this reaction. These steps are continued until every reaction of a modelled network is unambiguously annotated. The assertions presented are complemented by computational studies of a biochemical network for aerobic glycolysis. The fundamental premise of this work is that every row of a null space-generated subspace is a valid reaction and can therefore, be modelled as a reaction-specific sequence vector with a dimension that corresponds to the cardinality of the subspace after excluding all trivial- and redundant-vectors. A major finding of this study is that the row-wise sum or the sum of the terms contained in each reaction-specific sequence vector is mapped unambiguously to a positive real number. This means that the probable dissociation constants, for all reactions, can be directly computed from the stoichiometry number matrix and are suitable indicators of outcome for every reaction of the modelled biochemical network. Additionally, we find that the unambiguous annotation for a biochemical network will require a minimum number of iterations and will determine computational complexity.

Identification of an important QTL for seed oil content in soybean

Seed oil content is one of the most important quantitative traits in soybean (Glycine max) breeding. Here, we constructed a high-density single nucleotide polymorphism linkage map using two genetically similar parents, Heinong 84 and Kenfeng 17, that differ dramatically in their seed oil contents, and performed quantitative trait loci (QTL) mapping of seed oil content in a recombinant inbred line (RIL) population derived from their cross. We detected five QTL related to seed oil content distributed on five chromosomes. The QTL for seed oil content explained over 10% of the phenotypic variation over two years. This QTL was mapped to an interval containing 20 candidate genes, including a previously reported gene, soybean RING Finger 1a (RNF1a) encoding an E3 ubiquitin ligase. Notably, two short sequences were inserted in the GmRNF1a coding region of KF 17 compared to that of HN 84, resulting in a longer protein variant in KF 17. Our results thus provide information for uncovering the genetic mechanisms determining seed oil content in soybean, as well as identifying an additional QTL and highlighting GmRNF1a as candidate gene for modulating seed oil content in soybean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01384-2.

Genetic differentiation and genetic structure of mixed-ploidy Camellia hainanica populations

Camellia hainanica, which is common in China's Hainan Province, is an important woody olive tree species. Due to many years of geographic isolation, C. hainanica has not received the attention it deserves, which limits the exploitation of germplasm resources. Therefore, it is necessary to study population genetic characteristics for further utilization and conservation of C. hainanica. In this study, 96 individuals in six wild Camellia hainanica populations were used for ploidy analysis of the chromosome number, and the genetic diversity and population structure were investigated using 12 pairs of SSR primers. The results show complex ploidy differentiation in C. hainanica species. The ploidy of wild C. hainanica includes tetraploid, pentaploid, hexaploid, heptaploid, octoploid and decaploid species. Genetic analysis shows that genetic diversity and genetic differentiation among populations are low. Populations can be divided into two clusters based on their genetic structure, which matches their geographic location. Finally, to further maintain the genetic diversity of C. hainanica, ex-situ cultivation and in-situ management measures should be considered to protect it in the future.

Current status and trends in forest genomics

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

Integrating genome-wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus

Genome-wide association studies (GWAS) is a powerful and widely used approach to decipher the genetic control of complex traits. Still, a significant challenge for dissecting quantitative traits in forest trees is statistical power. This study uses a population consisting of 1,123 samples derived from two successive generations of crosses between Eucalyptus grandis (W. Hill) and E. urophylla (S.T. Blake). All samples have been phenotyped for growth and wood property traits and genotyped using the EuChip60K chip, yielding 37,832 informative single nucleotide polymorphisms (SNPs). We use multi-locus GWAS models to assess additive and dominance effects to identify markers associated with growth and wood property traits in the eucalypt hybrids. Additive and dominance association models identified 78 and 82 significant SNPs across all traits, respectively, which captured between 39 and 86% of the genomic-based heritability. We also used SNPs identified from the GWAS and SNPs using less stringent significance thresholds to evaluate predictive abilities in a genomic selection framework. Genomic selection models based on the top 1% SNPs captured a substantially greater proportion of the genetic variance of traits compared with when we used all SNPs for model training. The prediction ability of estimated breeding values improved significantly for all traits when using either the top 1% SNPs or SNPs identified using a relaxed p value threshold (p < 10^-3 ). This study also highlights the added value of incorporating dominance effects for identifying genomic regions controlling growth traits in trees. Moreover, integrating GWAS results into genomic selection method provides enhanced power relative to discrete associations for identifying genomic variation potentially valuable for forest tree breeding.

QTL mapping of drought-related traits in the hybrids of Populus deltoides 'Danhong'×Populus simonii 'Tongliao1'

BACKGROUND

Poplar trees provide a large amount of wood material, but many parts of the world are arid or semi-arid areas because of insufficient annual precipitation, which seriously affects the growth of poplar trees. Populus simonii 'Tongliao1' shows strong tolerance to stress environments, and Populus deltoides 'Danhong' shows a stronger growth rate in a suitable environment. To identify drought tolerance-related QTLs and genes, an F₁ population derived from the cross between the 'Danhong' and 'Tongliao 1' Populus was assessed under drought stress.

RESULTS

We measured drought-related traits such as the relative height growth, relative diameter growth, leaf senescence number, specific leaf area, and leaf relative water content in the population under control and drought environments. The results showed that drought stress reduced the plant height relative growth, ground diameter relative growth, specific leaf area and leaf relative water content and increased the number of leaf drops. A total of 208 QTLs were identified by QTL mapping analysis, and they consisted of 92, 63 and 53 QTLs under control, drought stress treatment and drought index conditions, respectively. A molecular identification marker for drought tolerance, np2841, which was associated with a QTL (qDLRWC-LG10-1) for relative leaf water content, was initially developed. We mined 187 candidate genes for QTL regions of five traits under a drought environment. The reference genome annotation for Populus trichocarpa and a homologous gene analysis of Arabidopsis thaliana identified two candidate genes, Potri.003G171300 and Potri.012G123900, with significant functions in response to drought stress. We identified five key regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) related to drought tolerance through the poplar coexpression network.

CONCLUSION

In this study, our results indicate that the QTLs can effectively enhance the drought tolerance of poplar. It is a step closer towards unravelling the genetic basis of poplar drought tolerance-related traits, and to providing validated candidate genes and molecular markers for future genetic improvement.

Time-sequential detection of quantitative trait loci and candidate genes underlying the dynamic growth of Salix suchowensis

Elucidating the genetic factors underlying long-term biological processes remains challenging since the relevant genes and their effects may vary across different developmental stages. In this study, we carried out a large-scale field trial of the progeny of an F1 full-sib pedigree of Salix suchowensis and measured plant height and ground diameter periodically over a time course of 240 days. With the obtained data, we characterized plant growth rhythms and performed time-sequential analyses of quantitative trait loci underlying the dynamic growth of the plants. The dynamic mapping of quantitative trait loci revealed that stem height and ground diameter were under the control of four quantitative trait loci, and the effects of these quantitative trait loci varied greatly throughout the growth process, in which two quantitative trait loci were found to exert a pleiotropic effect determining the correlation between stem height and ground diameter. The analysis of candidate genes in the target genetic intervals showed that the pleiotropic effect of the two quantitative trait loci arises from the colocalization of genes with independent effects on stem height and ground diameter. Further examination of the expression patterns of the candidate genes indicated that height and circumference growth involve different activities of leaf and cambium tissues. This study provides unprecedented information to help us understand the dynamic growth of plants and presents an applicable strategy for elucidating the genetic mechanism underlying a long-term biological process by using plant growth as an example.

Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L

Based on the integration of QTL-mapping and regulatory network analyses, five high-confidence stable QTL regions, six candidate genes and two microRNAs that potentially affect the cottonseed oil content were discovered. Cottonseed oil is increasingly becoming a promising target for edible oil with its high content of unsaturated fatty acids. In this study, a recombinant inbred line (RIL) cotton population was constructed to detect quantitative trait loci (QTLs) for the cottonseed oil content. A total of 39 QTLs were detected across eight different environments, of which five QTLs were stable. Forty-three candidate genes potentially involved in carbon metabolism, fatty acid synthesis and triacylglycerol biosynthesis processes were further obtained in the stable QTL regions. Transcriptome analysis showed that nineteen of these candidate genes expressed during  the developing cottonseed ovules and may affect the cottonseed oil content. Besides, transcription factor (TF) and microRNA (miRNA) co-regulatory network analyses based on the nineteen candidate genes suggested that six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TF GhHSL1 were considered to be closely associated with the cottonseed oil content. Moreover, four vital genes were validated by quantitative real-time PCR (qRT-PCR). These results provide insights into the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model.

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

High-Frequency Homologous Recombination Occurred Preferentially in Populus

Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

BACKGROUND

Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.

RESULTS

We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions.

CONCLUSIONS

In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.

Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design

With the advances in high-throughput sequencing technologies, it is not difficult to extract tens of thousands of single-nucleotide polymorphisms (SNPs) across many individuals in a fast and cheap way, making it possible to perform genome-wide association studies (GWAS) of quantitative traits in outbred forest trees. It is very valuable to apply traditional breeding experiments in GWAS for identifying genome variants associated with ecologically and economically important traits in Populus. Here, we reported a GWAS of tree height measured at multiple time points from a randomized complete block design (RCBD), which was established with clones from an F₁ hybrid population of Populus deltoides and Populus simonii. A total of 22,670 SNPs across 172 clones in the RCBD were obtained with restriction site-associated DNA sequencing (RADseq) technology. The multivariate mixed linear model was applied by incorporating the pedigree relationship matrix of individuals to test the association of each SNP to the tree heights over 8 time points. Consequently, 41 SNPs were identified significantly associated with the tree height under the P-value threshold determined by Bonferroni correction at the significant level of 0.01. These SNPs were distributed on all but two chromosomes (Chr02 and Chr18) and explained the phenotypic variance ranged from 0.26% to 2.64%, amounting to 63.68% in total. Comparison with previous mapping studies for poplar height as well as the candidate genes of these detected SNPs were also investigated. We therefore showed that the application of multivariate linear mixed model to the longitudinal phenotypic data from the traditional breeding experimental design facilitated to identify far more genome-wide variants for tree height in poplar. The significant SNPs identified in this study would enhance understanding of molecular mechanism for growth traits and would accelerate marker-assisted breeding programs in Populus.

Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions

The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of Eucalyptus cladocalyx, a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as GEM-related 5 and prohibitin-3, were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.

High-Quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus

With the advances in high-throughput sequencing technologies and the development of new software for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F₁ hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female P. deltoides map contained 4018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male P. simonii map showed similar characteristics, consisting of 2097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of P. simonii to chromosomes. The 2 parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.

Genome-wide association studies of callus differentiation for the desert tree, Populus euphratica

Callus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.

Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress

Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.

Linkage-linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus

Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. Linkage-linkage disequilibrium mapping was used to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F₁ progeny) and a natural population (435 unrelated individuals) of Populus using methylation-sensitive amplification polymorphism (MSAP)-based analysis. The interactions between genetic and epigenetic variants in the causative genes was further unveiled using expression quantitative trait methylation (eQTM) and nucleotide (eQTN) mapping strategies. A total of 163 epigenetic quantitative trait loci (epiQTLs; LOD ≥ 3.0), explaining 1.7-44.5% of phenotypic variations, were mapped to a high-resolution epigenetic map with 19 linkage groups, which was supported by the significant MSAP associations (P < 0.001) in the two populations. There were 23 causal genes involved in growth regulation and wood formation, whose markers were located in epiQTLs and associated with the same traits in both populations. Further eQTN and eQTM mapping showed that causal genetic and epigenetic variants within the 23 candidate genes may interact more in trans in gene expression and phenotype. The present study provides strategies for investigating epigenetic architecture and the interaction between genetic and epigenetic variants modulating complex traits in forest trees.

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.

An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.)

High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

BACKGROUND

Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.

RESULTS

Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F₁ population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.

CONCLUSIONS

This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)

BACKGROUND AND AIMS

Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea.

METHODS

A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits.

KEY RESULTS

Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots.

CONCLUSIONS

This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.

Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits

The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.

QTL analysis of nodule traits and the identification of loci interacting with the type III secretion system in soybean

Symbiotic nitrogen fixation is the main source of nitrogen for soybean growth. Since the genotypes of rhizobia and soybean germplasms vary, the nitrogen-fixing ability of soybean after inoculation also varies. A few studies have reported that quantitative trait loci (QTLs) control biological nitrogen fixation traits, even soybean which is an important crop. The present study reported that the Sinorhizobium fredii HH103 gene rhcJ belongs to the tts (type III secretion) cluster and that the mutant HH103ΩrhcJ can clearly decrease the number of nodules in American soybeans. However, few QTLs of nodule traits have been identified. This study used a soybean (Glycine max (L.) Merr.) 'Charleston' × 'Dongnong 594' (C × D, n = 150) recombinant inbred line (RIL). Nodule traits were analysed in the RIL population after inoculation with S. fredii HH103 and the mutant HH103ΩrhcJ. Plants were grown in a greenhouse with a 16-h light cycle at 26 °C and an 8-h dark cycle at 18 °C. Then, 4 weeks after inoculation, plants were harvested for evaluation of nodule traits. Through QTL mapping, 16 QTLs were detected on 8 chromosomes. Quantitative PCR (qRT-PCR) and RNA-seq analysis determined that the genes Glyma.04g060600, Glyma.18g159800 and Glyma.13g252600 might interact with rhcJ.

Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome-wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin-like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the "genes" into "genes to ecosystems ecology", this work enhances understanding of the molecular genetic mechanisms that underlie plant-insect associations and the consequences thereof for the structure of ecological communities.

Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)]

The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.

Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus

In perennial woody plants, the coordinated increase of stem height and diameter during juvenile growth improves competitiveness (i.e. access to light); however, the factors underlying variation in stem growth remain unknown in trees. Here, we used linkage-linkage disequilibrium (linkage-LD) mapping to decipher the genetic architecture underlying three growth traits during juvenile stem growth. We used two Populus populations: a linkage mapping population comprising a full-sib family of 1,200 progeny and an association mapping panel comprising 435 unrelated individuals from nearly the entire natural range of Populus tomentosa. We mapped 311 quantitative trait loci (QTL) for three growth traits at 12 timepoints to 42 regions in 17 linkage groups. Of these, 28 regions encompassing 233 QTL were annotated as 27 segmental homology regions (SHRs). Using SNPs identified by whole-genome re-sequencing of the 435-member association mapping panel, we identified significant SNPs (P ≤ 9.4 × 10^-7 ) within 27 SHRs that affect stem growth at nine timepoints with diverse additive and dominance patterns, and these SNPs exhibited complex allelic epistasis over the juvenile growth period. Nineteen genes linked to potential causative alleles that have time-specific or pleiotropic effects, and mostly overlapped with significant signatures of selection within SHRs between climatic regions represented by the association mapping panel. Five genes with potential time-specific effects showed species-specific temporal expression profiles during the juvenile stages of stem growth in five representative Populus species. Our observations revealed the importance of considering temporal genetic basis of complex traits, which will facilitate the molecular design of tree ideotypes.

Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations

Genome-wide association studies (GWAS) in plants typically suffer from limited statistical power. An alternative to the logistical and cost challenge of increasing sample sizes is to gain power by meta-analysis using information from independent studies. We carried out GWAS for growth traits with six single-marker models and regional heritability mapping (RHM) in four Eucalyptus breeding populations independently and by Joint-GWAS, using gene and segment-based models, with data for 3373 individuals genotyped with a communal EUChip60KSNP platform. While single-single nucleotide polymorphism (SNP) GWAS hardly detected significant associations at high-stringency in each population, gene-based Joint-GWAS revealed nine genes significantly associated with tree height. Associations detected using single-SNP GWAS, RHM and Joint-GWAS set-based models explained on average 3-20% of the phenotypic variance. Whole-genome regression, conversely, captured 64-89% of the pedigree-based heritability in all populations. Several associations independently detected for the same SNPs in different populations provided unprecedented GWAS validation results in forest trees. Rare and common associations were discovered in eight genes involved in cell wall biosynthesis and lignification. With the increasing adoption of genomic prediction of complex phenotypes using shared SNPs and much larger tree breeding populations, Joint-GWAS approaches should provide increasing power to pinpoint discrete associations potentially useful toward tree breeding and molecular applications.

Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects

Wood formation is an excellent model system for quantitative trait analysis due to the strong associations between the transcriptional and metabolic traits that contribute to this complex process. Investigating the genetic architecture and regulatory mechanisms underlying wood formation will enhance our understanding of the quantitative genetics and genomics of complex phenotypic variation. Genome-wide association studies (GWASs) represent an ideal statistical strategy for dissecting the genetic basis of complex quantitative traits. However, elucidating the molecular mechanisms underlying many favorable loci that contribute to wood formation and optimizing GWAS design remain challenging in this omics era. In this review, we summarize the recent progress in GWAS-based functional genomics of wood property traits in major timber species such as Eucalyptus, Populus, and various coniferous species. We discuss several appropriate experimental designs for extensive GWAS in a given undomesticated tree population, such as omics-wide association studies and high-throughput phenotyping technologies. We also explain why more attention should be paid to rare allelic and major structural variation. Finally, we explore the potential use of GWAS for the molecular breeding of trees. Such studies will help provide an integrated understanding of complex quantitative traits and should enable the molecular design of new cultivars.

Secondary Wall Regulating NACs Differentially Bind at the Promoter at a CELLULOSE SYNTHASE A4 Cis-eQTL

Arabidopsis thaliana CELLULOSE SYNTHASE A4/7/8 (CESA4/7/8) are three non-redundant subunits of the secondary cell wall cellulose synthase complex. Transcript abundance of these genes can vary among genotypes and expression quantitative trait loci (eQTL) were identified in a recombinant population of the accessions Bay-0 and Shahdara. Genetic mapping and analysis of the transcript levels of CESAs between two distinct near isogenic lines (NILs) confirmed a change in CESA4 expression that segregates within that interval. We sequenced the promoters and identified 16 polymorphisms differentiating CESA4^Sha and CESA4^Bay . In order to determine which of these SNPs could be responsible for this eQTL, we screened for transcription factor protein affinity with promoter fragments of CESA4^Bay, CESA4^Sha , and the reference genome CESA4^Col . The wall thickening activator proteins NAC SECONDARY WALL THICKENING PROMOTING FACTOR2 (NST2) and NST3 exhibited a decrease in binding with the CESA4^Sha promoter with a tracheary element-regulating cis-element (TERE) polymorphism. While NILs harboring the TERE polymorphisms exhibited significantly different CESA4 expression, cellulose crystallinity and cell wall thickness were indistinguishable. These results suggest that the TERE polymorphism resulted in differential transcription factor binding and CESA4 expression; yet A. thaliana is able to tolerate this transcriptional variability without compromising the structural elements of the plant, providing insight into the elasticity of gene regulation as it pertains to cell wall biosynthesis and regulation. We also explored available DNA affinity purification sequencing data to resolve a core binding site, C(G/T)TNNNNNNNA(A/C)G, for secondary wall NACs referred to as the VNS element.

Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar

High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar. Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics. Here, we generated a high-quality and dense genetic map for an F1 poplar population using high-throughput NGS-based genotyping. A total of 92,097 high-quality SNP markers were developed by stringent filtering and identification. In total, 889 and 1650 SNPs formed the female and male genetic maps, respectively. To test the application of the genetic maps, QTL mapping of leaf shape was conducted for this F1 population. A total of nine parameters were scored for leaf shape variation in three different environments. Combining genetic maps and measurements of the nine leaf shape parameters, we mapped a total of 42 significant QTLs. The highest LOD score of all QTLs was 9.2, and that QTL explained the most (15.13%) trait variation. A total of nine QTLs could be detected in at least two environments, and they were located in two genomic regions. Within these two QTL regions, some candidate genes for regulating leaf shape were predicted through functional annotation. The successful mapping of leaf shape QTLs demonstrated the utility of our genetic maps. According to the performance of this study, we were able to provide high-quality and dense genetic maps and dissect the leaf shape variation in poplar.

Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis

Suitability of wood biomass for pulp production is dependent on the cellular architecture and composition of secondary cell wall. Presently, systems genetics approach is being employed to understand the molecular basis of trait variation and co-expression network analysis has enabled holistic understanding of complex trait such as secondary development. Transcription factors (TFs) are reported as key regulators of meristematic growth and wood formation. The hierarchical TF network is a multi-layered system which interacts with downstream structural genes involved in biosynthesis of cellulose, hemicelluloses and lignin. Several TFs have been associated with wood formation in tree species such as Populus, Eucalyptus, Picea and Pinus. However, TF-specific co-expression networks to understand the interaction between these regulators are not reported. In the present study, co-expression network was developed for TFs expressed during wood formation in Eucalyptus tereticornis and ethylene-responsive element-binding factor, EtERF2, was identified as the major hub transcript which co-expressed with other secondary cell wall biogenesis-specific TFs such as EtSND2, EtVND1, EtVND4, EtVND6, EtMYB70, EtGRAS and EtSCL8. This study reveals a probable role of ethylene in determining natural variation in wood properties in Eucalyptus species. Understanding this transcriptional regulation underpinning the complex bio-processing trait of wood biomass will complement the Eucalyptus breeding program through selection of industrially suitable phenotypes by marker-assisted selection.

Thirteen years under arid conditions: exploring marker-trait associations in Eucalyptus cladocalyx for complex traits related to flowering, stem form and growth

We present an association analysis for seven key traits related to flowering, stem form and growth in Eucalyptus cladocalyx, a tree species suitable for low rainfall sites, using a long-term progeny trial with 49 open-pollinated maternal families in the southern Atacama Desert, Chile. The progeny trial was carried out in an arid environment with a mean annual rainfall of 152 mm. Simple sequence repeats (SSR) from a full consensus map of Eucalyptus were used for genotyping 245 individual trees. Twenty-three significant marker-trait associations were identified, explaining between 5.9 and 23.7% of the phenotypic variance. The marker EMBRA101 located on LG10 at 56.5 cM was concomitantly associated with diameter at breast height and tree height. Nine SSR were significantly associated with stem forking and stem straightness, explaining between 5.9 and 14.8% of the phenotypic variation. To our knowledge, this is the first study reporting a SSR-based association mapping analysis for stem form traits in Eucalyptus. These results provide novel and valuable information for understanding the genetic base of key traits in E. cladocalyx for breeding purposes under arid conditions.

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

Background

Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are maternally inherited, but the chloroplast’ variation pattern of poplar at the single-base level during the transmission from mother to offspring remains unknown.

Results

Here, we constructed high-quality and almost complete chloroplast genomes for three poplar clones, ‘NL895’ and its parents, ‘I69’ and ‘I45’, from the short-read datasets using multi-pass sequencing (15–16 times per clone) and ultra-high coverage (at least 8500× per clone), with the four-step strategy of Simulation–Assembly–Merging–Correction. Each of the three resulting chloroplast assemblies contained contigs covering > 99% of Populus trichocarpa chloroplast DNA as a reference. A total of 401 variant loci were identified by a hybrid strategy of genome comparison-based and mapping-based single nucleotide polymorphism calling. The genotypes of 94 variant loci were different among the three poplar clones. However, only 1 of the 94 loci was a missense mutation, which was located in the exon region of rpoC1 encoding the β’ subunit of plastid-encoded RNA polymerase. The genotype of the loci in NL895 and its female parent (I69) was different from that of its male parent (I45).

Conclusions

This research provides resources for further chloroplast genomic studies of a F₁ full-sibling family derived from a cross between I69 and I45, and will improve the application of chloroplast genomic information in modern Populus breeding programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4813-8) contains supplementary material, which is available to authorized users.

Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume

Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I^∗ = 0.575, h^∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.

MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species

Background

With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F₁ population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines.

Results

We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F₁ population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations.

Conclusions

We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F₁ population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim.

Electronic supplementary material

The online version of this article (10.1186/s12859-017-1908-1) contains supplementary material, which is available to authorized users.

Genetic Characterization of Chinese fir from Six Provinces in Southern China and Construction of a Core Collection

Large ex situ germplasm collections of plants generally contain significant diversity. A set of 700 well-conserved Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) clones from six provinces in southern China in the ex situ gene bank of Longshan State Forest, was analyzed using 21 simple sequence repeat markers, with the aim of assessing the genetic diversity of these germplasm resources. Genetic analysis revealed extensive genetic variation among the accessions, with an average of 8.31 alleles per locus and a mean Shannon index of 1.331. Excluding loci with null alleles, we obtained a low level of genetic differentiation among provinces, consistent with the interpopulation genetic variation (1%). Three clusters were identified by STRUCTURE, which did not match the individuals’ geographical provenances. Ten traits related to growth and wood properties were quantified in these individuals, and there was substantial variation in all traits across individuals, these provide a potential source of variation for genetic improvement of the Chinese fir. Screening large collections for multiple-trait selective breeding programs is laborious and expensive; a core collection of 300 accessions, representative of the germplasm, was established, based on genotypic and phenotypic data. The identified small, but diverse, collections will be useful for further genome-wide association studies.

Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa

Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.

Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds

Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log₂ (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels and CNV.

Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

Background

The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses.

Results

Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000–10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range historical linkage disequilibrium (LD) was likely captured for E. pellita. A GWAS identified only one significant association for volume growth in E. pellita, illustrating the fact that while genome-wide regression is able to account for large proportions of the heritability, very little or none of it is captured into significant associations using GWAS in breeding populations of the size evaluated in this study.

Conclusions

This study provides further experimental data supporting positive prospects of using genome-wide data to capture large proportions of trait heritability and predict growth traits in trees with accuracies equal or better than those attainable by phenotypic selection. Additionally, our results document the superiority of the whole-genome regression approach in accounting for large proportions of the heritability of complex traits such as growth in contrast to the limited value of the local GWAS approach toward breeding applications in forest trees.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3920-2) contains supplementary material, which is available to authorized users.

Functional natural allelic variants of flavonoid 3',5'-hydroxylase gene governing catechin traits in tea plant and its relatives

Functional allelic variants of the flavonoid 3',5'-hydroxylase (F3'5'H) gene provides new information of F3'5'H function of tea plant and its relatives. This insight may serve as the foundation upon which to advance molecular breeding in the tea plant. Catechins are the active components of tea that determine its quality and health attributes. This study established the first integrated genomic strategy for deciphering the genetic basis of catechin traits of tea plant. With the RNA-sequencing analysis of bulked segregants representing the tails of a F1 population segregated for total catechin content, we identified a flavonoid 3',5'-hydroxylase (F3'5'H) gene. F3'5'H had one copy in the genomic DNA of tea plant. Among 202 tea accessions, we identified 120 single nucleotide polymorphisms (SNPs) at F3'5'H locus. Seventeen significant marker-trait associations were identified by association mapping in multiple environments, which were involved in 10 SNP markers, and the traits including the ratio of di/tri-hydroxylated catechins and catechin contents. The associated individual and combination of SNPs explained 4.5-25.2 and 53.0-63.0% phenotypic variations, respectively. In the F1 population (validation population), the catechin trait variation percentages explained by F3'5'H diplotype were 6.9-74.3%. The genotype effects of ten functional SNPs in the F1 population were all consistent with the association population. Furthermore, the function of SNP-711/-655 within F3'5'H was validated by gene expression analysis. Altogether, our work indicated functional SNP allelic variants within F3'5'H governing the ratio of di/tri-hydroxylated catechins and catechin contents. The strong catechin-associated SNPs identified in this study can be used for future marker-assisted selection to improve tea quality.

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

Background

Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches.

Results

The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait.

Conclusions

This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.

PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants

Poplar is not only an important resource for the production of paper, timber and other wood-based products, but it has also emerged as an ideal model system for studying woody plants. To better understand the biological processes underlying various traits in poplar, e.g., wood development, a comprehensive functional gene interaction network is highly needed. Here, we constructed a genome-wide functional gene network for poplar (covering ~70% of the 41,335 poplar genes) and created the network web service PoplarGene, offering comprehensive functional interactions and extensive poplar gene functional annotations. PoplarGene incorporates two network-based gene prioritization algorithms, neighborhood-based prioritization and context-based prioritization, which can be used to perform gene prioritization in a complementary manner. Furthermore, the co-functional information in PoplarGene can be applied to other woody plant proteomes with high efficiency via orthology transfer. In addition to poplar gene sequences, the webserver also accepts Arabidopsis reference gene as input to guide the search for novel candidate functional genes in PoplarGene. We believe that PoplarGene (http://bioinformatics.caf.ac.cn/PoplarGene and http://124.127.201.25/PoplarGene) will greatly benefit the research community, facilitating studies of poplar and other woody plants.