Nutrient allocation patterns of Picea crassifolia on the eastern margin of the Qinghai-Tibet Plateau.

It can provide a basis for decision making for the conservation and sustainable use of forest ecosystems in mountains to understand the stoichiometric properties and nutrient allocation strategies of major tree species. However, the plant nutrient allocation strategies under different environmental gradients in forest systems of arid and semi-arid mountains are not fully understand. Therefore, three typical regions in the Qilian Mountains on the eastern edge of the Qinghai-Tibet Plateau were selected based on precipitation and temperature gradients, and the stoichiometric characteristics and nutrient allocation strategies of Qinghai spruce (Picea crassifolia) of the dominant tree species under different environmental gradients were investigated. The results showed that (1) the stoichiometric characteristics of plant tissues were different in the three regions. (2) The importance of each tissue in the plant nutrient allocation varied in different regions, showing that the plant roots are more important in the warm-wet region, while the plant leaves, branches and trunks are more important in the transition and hot-dry regions. (3) The influencing factors affecting plant nutrient allocation strategies were inconsistent across regions, which showed that plant nutrient allocation strategies in the warm-wet and transition region were mainly influenced by soil factors, while they were more influenced by climatic factors in the hot-dry region. The patterns of plant nutrient allocation strategies and drivers under different environmental gradients could help us better understand the ecological adaptation mechanism and physiological adjustment mechanism of forest ecosystem in mountains.

Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping.

Introduction: Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging. Methods: In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions. Results: By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1. Discussion: By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Hormonal Regulation and Stimulation Response of Jatropha curcas L. Homolog Overexpression on Tobacco Leaf Growth by Transcriptome Analysis.

The Flowering locus T (FT) gene encodes the florigen protein, which primarily regulates the flowering time in plants. Recent studies have shown that FT genes also significantly affect plant growth and development. The FT gene overexpression in plants promotes flowering and suppresses leaf and stem development. This study aimed to conduct a transcriptome analysis to investigate the multiple effects of Jatropha curcas L. homolog (JcFT) overexpression on leaf growth in tobacco plants. The findings revealed that JcFT overexpression affected various biological processes during leaf development, including plant hormone levels and signal transduction, lipid oxidation metabolism, terpenoid metabolism, and the jasmonic-acid-mediated signaling pathway. These results suggested that the effects of FT overexpression in plants were complex and multifaceted, and the combination of these factors might contribute to a reduction in the leaf size. This study comprehensively analyzed the effects of JcFT on leaf development at the transcriptome level and provided new insights into the function of FT and its homologous genes.

Spatial characteristics of nutrient allocation for Picea crassifolia in soil and plants on the eastern margin of the Qinghai-Tibet Plateau.

BACKGROUND: Understanding the stoichiometric characteristics and nutrient allocation strategies of dominant tree species in montane forest systems can provide a basis for decision-making in relation to montane system management. Therefore, according to precipitation and temperature gradients, we selected three typical areas in the Qilian Mountains on the eastern margin of the Qinghai-Tibet Plateau to analyse the spatial relations of plant-soil stoichiometric characteristics and nutrient allocation strategies of plant tissues for Qinghai spruce (Picea crassifolia) along different environmental gradients. RESULTS: 1) The plant and soil stoichiometric characteristics had similar spatial patterns. The C content of plants and soils tended to decrease with increasing latitude, and the N and P contents and the N:P ratio tended to increase with increasing latitude. 2) The stoichiometric characteristics of the plant tissues also interacted with each other and showed synergistic trade-offs. Nutrient allocation in the eastern section of the Qilian Mountains was similar to that in the western section, while more N and P in the plant stems were allocated to maintain plant growth in the relatively arid western Sect. 3) The nutrient allocation strategies in the plant tissues were mainly regulated by soil and climate. CONCLUSIONS: Information on plant-soil stoichiometric characteristics along different gradients can help us better understand the nutrient patterns and dynamics of forest ecosystems under arid and semiarid conditions at a wide geographic scale from the perspective of plant nutrient partitioning.

Future Fertility of Patients With No Embryo Transfer in Their First IVF Cycle Attempts.

Objective: We aimed to evaluate the future outcomes of patients undergoing their first IVF (in vitro fertilization) attempt with no oocyte retrieved, no normal zygotes formed, or no embryos available for transfer and to identify factors affecting the live birth rate. Methods: Patients who underwent no transplantable embryo in their first IVF cycles but carried out several consecutive cycles between January 2012 to December 2020 were retrospectively enrolled and divided into three groups:group A (no egg retrieval), group B (no normal zygotes formed), and group C (no embryos available to transfer). The patients were also divided into the live birth group and non-live birth group according to whether they got a live baby or not. The clinical data and the cumulative clinical outcomes of groups were compared. Results: 496 patients met the inclusion criteria and enrolled, with 121 patients with no oocytes retrieved in group A, 138 patients with no normal zygotes formed in group B, and 237 patients with no embryos available to transfer in group C. The age [(34.75(5.82) vs 31.91(5.31), P<0.001; 34.75(5.82) vs 32.25(5.72), P<0.001)] and baseline FSH level [(13.04(8.82) vs 10.52(7.39), P=0.005; 13.04(8.82) vs 9.91(5.95), P<0.001)] of women in group A were significantly higher than those in groups B and C. The stable cumulative live birth rate/patient of three groups achieved 18.18% (after 5 cycles, group A), 28.98% (after 3 cycles, group B) and 20.25% (after 7 cycles, group C). Moreover, the multivariate regression analysis showed that female age and basic FSH were main factors affecting live birth outcome of patients with no embryo transfer in their first IVF cycle attempts. Conclusions: The future clinical outcome may be better in women with no normal zygotes than those with no oocyte retrieved or no available embryo at their first IVF cycle attempts. The main factors influencing the live birth are age and ovarian reserve.

The Optimal Number of Oocytes Retrieved From PCOS Patients Receiving IVF to Obtain Associated With Maximum Cumulative Live Birth Rate and Live Birth After Fresh Embryo Transfer.

Aims: This study aims to determine the optimal number of oocytes retrieved so that patients with polycystic ovary syndrome (PCOS) receiving in vitro fertilization (IVF) can obtain the best cumulative live birth rate (CLBR) and live birth after fresh embryo transfer. Methods: This is a retrospective study of 1,419 patients with PCOS who underwent their first IVF cycle at the Second Hospital of Hebei Medical University from January 2014 to December 2021. Multivariable regression analysis was performed to adjust for factors known to independently affect cumulative live birth aspiration. The number of oocytes retrieved to obtain the best cumulative live birth rate was explored through curve fitting and threshold effect analysis. The decision tree method was used to explore the best number of oocytes retrieved to achieve live birth in the shortest time. Results: (1) The number of oocytes retrieved was found to be an independent protective factor for the cumulative live birth rate (OR = 1.09 (95% CI: 1.06, 1.12)). When the number of oocytes retrieved was less than 15, CLBR increased by 16% with each increase in the number of oocytes retrieved (OR = 1.16 (95% CI: 1.11, 1.22)); and when more than 15, CLBR tended to be stable. (2) Live birth after the first fresh embryo transfer was analyzed through a classification decision tree. For patients younger than 35 years old, those with less than 6 oocytes and those with 7-16 oocytes had a similar proportion of live births with fresh embryo transfer but higher than 16 oocytes (53.7% vs. 53.8% vs. 18.4%). Patients older than 35 years old had a similar proportion of live births with fresh embryo transfer (35.7% vs. 39.0%) to those younger than 35 years old, but the proportion of no live births after using up all embryos was higher than those younger than 35 years old (39.3% vs. 19.2%). Conclusions: In PCOS patients, high CLBR can be obtained when the number of oocytes retrieved was 15 or more. The number of oocytes retrieved from 7 to 16 could achieve more chance of live birth after fresh embryo transfer.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco.

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFTOE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFTOE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFTOE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFTOE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFTOE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFTOE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFTOE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFTOE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFTOE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica.

Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica, which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica. Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.

Genome-Wide Identification and Analysis of the NAC Transcription Factor Gene Family in Garden Asparagus (Asparagus officinalis).

As a large plant-specific gene family, the NAC (NAM, ATAF1/2, and CUC2) transcription factor is related to plant growth, development, and response to abiotic stresses. Although the draft genome of garden asparagus (Asparagus officinalis) has been released, the genome-wide investigation of the NAC gene family is still unavailable. In this study, a total of 85 A. officinalis NAC genes were identified, and a comprehensive analysis of the gene family was performed, including physicochemical properties, phylogenetic relationship, chromosome localization, gene structure, conserved motifs, intron/exon, cis-acting elements, gene duplication, syntenic analysis, and differential gene expression analysis. The phylogenetic analysis demonstrated that there were 14 subgroups in both A. officinalis and Arabidopsis thaliana, and the genes with a similar gene structure and motif distribution were clustered in the same group. The cis-acting regulatory analysis of AoNAC genes indicated four types of cis-acting elements were present in the promoter regions, including light-responsive, hormone-responsive, plant-growth-and-development-related, and stress-responsive elements. The chromosomal localization analysis found that 81 NAC genes in A. officinalis were unevenly distributed on nine chromosomes, and the gene duplication analysis showed three pairs of tandem duplicated genes and five pairs of segmental duplications, suggesting that gene duplication is possibly associated with the amplification of the A. officinalis NAC gene family. The differential gene expression analysis revealed one and three AoNAC genes that were upregulated and downregulated under different types of salinity stress, respectively. This study provides insight into the evolution, diversity, and characterization of NAC genes in garden asparagus and will be helpful for future understanding of their biological roles and molecular mechanisms in plants.

PTX3/TWIST1 Feedback Loop Modulates Lipopolysaccharide-Induced Inflammation via PI3K/Akt Signaling Pathway.

Chronic inflammation of nasal mucosal tissue is an obvious feature of allergic rhinitis. Pentraxin 3 (PTX3) is a member of the pentraxin family and plays important roles in inflammation. We aimed to investigate the roles and mechanisms of PTX3 in inflammatory factors and MUC5AC production in human nasal epithelia cells. Loss- and gain-of-function experiments were performed. We found that the silencing of PTX3 dramatically blocked the expression of interleukin (IL)-6, IL-8, IL-1ß, and MUC5AC induced by lipopolysaccharide (LPS). Gain-of-function of PTX3 displayed the opposite results. Interestingly, the ablation of PTX3 blocked activation of the PI3K/Akt signaling pathway, whereas the administration of an agonist of PI3K, 740Y-P, partially reversed the inhibitory functions of PTX3 silencing on inflammation and MUC5AC production. Moreover, PTX3 was a positive regulator of TWIST1, which is one of the transcription factors of PTX3. We noticed that TWIST1 downregulation reduced the expression of PTX3. Furthermore, chromatin immunoprecipitation assay and dual-luciferase reporter assay demonstrated that TWIST1 could bind to the promoter of PTX3. Importantly, the depletion of TWIST1 attenuated the LPS-mediated expression and secretion of inflammatory cytokines, whereas these effects were partially abolished upon PTX3 overexpression. Taken together, our findings revealed that the PTX3/TWIST1 feedback loop modulates LPS-induced inflammation and MUC5AC production via the PI3K/Akt signaling pathway.

A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits.

The effects of genes on physiological and biochemical processes are interrelated and interdependent; it is common for genes to express pleiotropic control of complex traits. However, the study of gene expression and participating pathways in vivo at the whole-genome level is challenging. Here, we develop a coupled regulatory interaction differential equation to assess overall and independent genetic effects on trait growth. Based on evolutionary game theory and developmental modularity theory, we constructed multilayer, omnigenic networks of bidirectional, weighted, and positive or negative epistatic interactions using a forest poplar tree mapping population, which were organized into metagalactic, intergalactic, and local interstellar networks that describe layers of structure between modules, submodules, and individual single nucleotide polymorphisms, respectively. These multilayer interactomes enable the exploration of complex interactions between genes, and the analysis of not only differential expression of quantitative trait loci but also previously uncharacterized determinant SNPs, which are negatively regulated by other SNPs, based on the deconstruction of genetic effects to their component parts. Our research framework provides a tool to comprehend the pleiotropic control of complex traits and explores the inherent directional connections between genes in the structure of omnigenic networks.

A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions.

Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.

Genetic Architecture of Multiphasic Growth Covariation as Revealed by a Nonlinear Mixed Mapping Framework.

Trait covariation during multiphasic growth is of crucial significance to optimal survival and reproduction during the entire life cycle. However, current analyses are mainly focused on the study of individual traits, but exploring how genes determine trait interdependence spanning multiphasic growth processes remains challenging. In this study, we constructed a nonlinear mixed mapping framework to explore the genetic mechanisms that regulate multiphasic growth changes between two complex traits and used this framework to study stem diameter and stem height in forest trees. The multiphasic nonlinear mixed mapping framework was implemented in system mapping, by which several key quantitative trait loci were found to interpret the process and pattern of stem wood growth by regulating the ecological interactions of stem apical and lateral growth. We quantified the timing and pattern of the vegetative phase transition between independently regulated, temporally coordinated processes. Furthermore, we visualized the genetic machinery of significant loci, including genetic effects, genetic contribution analysis, and the regulatory relationship between these markers in the network structure. We validated the utility of the new mapping framework experimentally via computer simulations. The results may improve our understanding of the evolution of development in changing environments.

Modeling genome-wide by environment interactions through omnigenic interactome networks.

How genes interact with the environment to shape phenotypic variation and evolution is a fundamental question intriguing to biologists from various fields. Existing linear models built on single genes are inadequate to reveal the complexity of genotype-environment (G-E) interactions. Here, we develop a conceptual model for mechanistically dissecting G-E interplay by integrating previously disconnected theories and methods. Under this integration, evolutionary game theory, developmental modularity theory, and a variable selection method allow us to reconstruct environment-induced, maximally informative, sparse, and casual multilayer genetic networks. We design and conduct two mapping experiments by using a desert-adapted tree species to validate the biological application of the model proposed. The model identifies previously uncharacterized molecular mechanisms that mediate trees' response to saline stress. Our model provides a tool to comprehend the genetic architecture of trait variation and evolution and trace the information flow of each gene toward phenotypes within omnigenic networks.

The optimal number of embryo cells for effective pregnancy and decrease of multiple pregnancy rate in frozen-thawed embryo transfer.

To investigate the effect of the number of embryo cells on the clinical outcome of frozen-thawed embryo transfer and explore the optimal policy for decreases of multiple pregnancy rate, patients who experienced day 3 vitrified double frozen-thawed embryo transfer were retrospectively analyzed. According to the number of embryonic cells in each pre-frozen embryo, the patients were divided into six groups: 8C2 (two 8-cell embryos), 8C1- < 8C1 (one 8-cell embryo and one under-8-cell embryo), 8C1- > 8C1 (one 8-cell embryo and one over-8-cell embryo), < 8C2 (two under-8-cell embryos), < 8C1- > 8C1 (one under-8-cell embryo and one over-8-cell embryo), and > 8C2 (two over-8-cell embryos). The clinical data were analyzed. The classification decision tree was used to analyze the optimal transfer strategy. A total of 2184 cycles of day 3 vitrified double frozen-thawed embryo transfer were enrolled. In day 3 double frozen-thawed embryo cycles, the 8C2 group and 8C1- > 8C1 group had significantly (P < 0.05) higher pregnancy and multiple pregnancy rates than the other groups. No significant (P > 0.05) difference existed in the pregnancy rate and live birth rate between the 8C1- < 8C1 group, 8C2 group and 8C1- > 8C1 group, but the implantation rate and multiple pregnancy rate in the 8C1- < 8C1 group were significantly (P < 0.05) lower than in the other two groups. Compared with the multiple pregnancy rate of all cycles, the cycles in two branches showed significantly (P < 0.05) higher multiple pregnancy rates (≤ 29 years old: 8C2 / 8C1- > 8C1; 29 < age ≤ 36 years for the first transfer: 8C2 / 8C1- < 8C1 / 8C1- > 8C1, one branch showed similar rate (≤ 29 years old: 8C2 / 8C1- > 8C1) for the first transfer, and the remaining four branches demonstrated significantly (P < 0.05) lower rates. The clinical pregnancy rates before and after optimization were 51.0% vs 50.5%, and the multiple pregnancy rates were 38.5% vs 16.9%. In conclusion, the number of pre-frozen embryonic cells is an important factor affecting the clinical outcome of frozen-thawed embryo transfer in day 3 double good embryos frozen-thawed cycles. The age of patient, number of embryo cells, and the first time of transfer are the most valuable parameters for prediction. For women ≤ 29 years old, the single embryo transfer (SET) strategy was to choose an embryo ≥ 8 cells, and for women with < 29 age ≤ 36 years old, the SET strategy in the first transfer was to choose an embryo ≥ 8 cells.

Identification of Quantitative Trait Loci for Altitude Adaptation of Tree Leaf Shape With Populus szechuanica in the Qinghai-Tibetan Plateau.

As an important functional organ of plants, leaves alter their shapes in response to a changing environment. The variation of leaf shape has long been an important evolutionary and developmental force in plants. Despite an increasing amount of investigations into the genetic controls of leaf morphology, few have systematically studied the genetic architecture controlling shape differences among distinct altitudes. Altitude denotes a comprehensive complex of environmental factors affecting plant growth in many aspects, e.g., UV-light radiation, temperature, and humidity. To reveal how plants alter ecological adaptation to altitude through genes, we used Populus szechuanica var. tibetica growing on the Qinghai-Tibetan plateau. F ST between the low- and high- altitude population was 0.00748, Q ST for leaf width, length and area were 0.00924, 0.1108, 0.00964 respectively. With the Elliptic Fourier-based morphometric model, association study of leaf shape was allowed, the dissection of the pleiotropic expression of genes mediating altitude-derived leaf shape variation was performed. For high and low altitudes, 130 and 131 significant single-nucleotide polymorphisms (SNPs) were identified. QTLs that affected leaf axis length and leaf width were expressed in both-altitude population, while QTLs regulating "leaf tip" and "leaf base" were expressed in low-altitude population. Pkinase and PRR2 were common significant genes in both types of populations. Auxin-related and differentiation-related genes included PIN1, CDK-like, and CAK1AT at high altitude, whereas they included NAP5, PIN-LIKES, and SCL1 at low altitude. The presence of Stress-antifung gene, CIPK3 and CRPK1 in high-altitude population suggested an interaction between genes and harsh environment in mediating leaf shape, while the senescence repression-related genes (EIN2 and JMJ18) and JMT in jasmonic acid pathway in low-altitude population suggested their crucial roles in ecological adaptability. These data provide new information that strengthens the understanding of genetic control with respect to leaf shape and constitute an entirely novel perspective regarding leaf adaptation and development in plants.

Corrigendum: A Computational Model for Inferring QTL Control Networks Underlying Developmental Covariation.

[This corrects the article DOI: 10.3389/fpls.2019.01557.].

The Genomic Landscape of Crossover Interference in the Desert Tree Populus euphratica.

Crossover (CO) interference is a universal phenomenon by which the occurrence of one CO event inhibits the simultaneous occurrence of other COs along a chromosome. Because of its critical role in the evolution of genome structure and organization, the cytological and molecular mechanisms underlying CO interference have been extensively investigated. However, the genome-wide distribution of CO interference and its interplay with sex-, stress-, and age-induced differentiation remain poorly understood. Multi-point linkage analysis has proven to be a powerful tool for landscaping CO interference, especially within species for which CO mutants are rarely available. We implemented four-point linkage analysis to landscape a detailed picture of how CO interference is distributed through the entire genome of Populus euphratica, the only forest tree that can survive and grow in saline desert. We identified an extensive occurrence of CO interference, and found that its strength depends on the length of chromosomes and the genomic locations within the chromosome. We detected high-order CO interference, possibly suggesting a highly complex mechanism crucial for P. euphratica to grow, reproduce, and evolve in its harsh environment.

np2 QTL: networking phenotypic plasticity quantitative trait loci across heterogeneous environments.

Despite its critical importance to our understanding of plant growth and adaptation, the question of how environment-induced plastic response is affected genetically remains elusive. Previous studies have shown that the reaction norm of an organism across environmental index obeys the allometrical scaling law of part-whole relationships. The implementation of this phenomenon into functional mapping can characterize how quantitative trait loci (QTLs) modulate the phenotypic plasticity of complex traits to heterogeneous environments. Here, we assemble functional mapping and allometry theory through Lokta-Volterra ordinary differential equations (LVODE) into an R-based computing platform, np2 QTL, aimed to map and visualize phenotypic plasticity QTLs. Based on LVODE parameters, np2 QTL constructs a bidirectional, signed and weighted network of QTL-QTL epistasis, whose emergent properties reflect the ecological mechanisms for genotype-environment interactions over any range of environmental change. The utility of np2 QTL was validated by comprehending the genetic architecture of phenotypic plasticity via the reanalysis of published plant height data involving 3502 recombinant inbred lines of maize planted in multiple discrete environments. np2 QTL also provides a tool for constructing a predictive model of phenotypic responses in extreme environments relative to the median environment.

A unified DNA sequence and non-DNA sequence mapping model of complex traits.

Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non-DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open-pollinated design composed of randomly sampling maternal plants from a natural population and their half-sib seeds. This design forms a two-level hierarchical platform for a joint linkage-linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence-based effects and non-DNA sequence-based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non-DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA-based effects and non-DNA sequence-based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.